Modified nucleotides methods and kits

ABSTRACT

Modified nucleotides, and methods to modify nucleotides with a moiety or label, such as biotin, that permits their detection and results in a modified nucleotide, and methods of use of the modified nucleotide in quantitative and qualitative assays.

This application is a divisional of U.S. application Ser. No.14/883,810, filed Oct. 15, 2015, which is a divisional of U.S.application Ser. No. 13/482,927, filed May 29, 2012, now U.S. Pat. No.9,206,216, which is a Continuation-in-Part of co-pending U.S.application Ser. No. 13/090,729 filed Apr. 20, 2011, now U.S. Pat. No.8,536,323, which claims priority from U.S. Provisional application Ser.No. 61/326,450 filed Apr. 21, 2010, all of which are expresslyincorporated by reference herein in their entirety.

INCORPORATION OF SEQUENCE LISTING

The present application contains a Sequence Listing in electronicformat. The Sequence Listing is provided as a file entitled“2018-01-19_01129-0032-03US_SeqList_ST25.txt” created on Jan. 19, 2018,which is 1,182 bytes in size. The information in the electronic formatof the sequence listing is incorporated herein by reference in itsentirety.

Modified nucleotides, methods to modify nucleotides with a moiety orlabel, such as biotin, that permit their detection and result in amodified nucleotide, methods of use of the modified nucleotide inquantitative and qualitative assays, and methods of synthesizing thedisclosed modified nucleotides.

The modified nucleotides have the structure P1-P2-Nus-Alk-Lnk-Obs, andinclude a salt, conjugate base, tautomer, or ionized form, where P1 is aphosphate group; P2 is a phosphate group; Nus is a nucleoside moietycomprising a sugar bound to a purine or pyrimidine base; Alk is aconnecting group having the structure -//—(CH₂)_(m)—Y—//- where Y is abond or bond forming group selected from

andm is an integer ranging from 3 to 6 inclusive, and where the leftmostbond is to Nus and the rightmost bond is to Lnk; Lnk is a linking grouphaving the structure

where n is an integer ranging from 2 to 48 inclusive; A₁ is a bondforming group selected from

A₂ is a bond forming group selected from

A₃, when present, is a bond forming group selected from

X is a cleavable group that can undergo silicon-carbon cleavage,nucleophilic cleavage, redox cleavage, photochemical cleavage, enzymaticcleavage, or exchange-based cleavage, and the leftmost bond is to Alkand the rightmost bond is to Obs; and Obs is an observable label moiety.

Such modified nucleotides, also termed nucleotide analogs, retainbiological activity. For example, they are substrates for a variety ofDNA and/or RNA polymerases. The modified nucleotide is added to anoligonucleotide or nucleic acid by routine methods, e.g., nicktranslation, random priming, polymerase chain reaction (PCR), 3′-endlabeling, transcribing RNA using SP6, T3, or T7 RNA polymerases, etc.

Modified nucleotides may be used to form labeled probes that may be usedin, e.g., biological screening, diagnosis, etc. As one example,screening an array permits different constituents of a complex sample tobe determined. For example, an oligonucleotide probe containing abiotinylated nucleotide specifically binds to analytes in the samplethat contain a complementary sequence, yielding an observable bindingpattern detectable upon interrogating the array. As another example, anoligonucleotide probe containing a biontinylated nucleotide can be usedto investigate small ribonucleic acids (RNAs) such as microRNAs(miRNAs), and their functional interactions with other RNA molecules orcellular proteins.

BRIEF DESCRIPTION OF THE DRAWINGS

The patent or application file contains at least one drawing executed incolor. Copies of this patent or patent application publication withcolor drawing(s) will be provided by the Office upon request and paymentof the necessary fee.

FIG. 1 shows synthesis of biotin-polyethylene glycol(PEG)-alkane-3′,5′-cytidine bisphosphate.

FIG. 2 shows synthesis of biotin-linker-alkyne-3′, 5′ cytidinebisphosphate.

FIG. 3 shows synthesis of biotin-linker-alkene 3′, 5′ cytidinebisphosphate.

FIG. 4 shows functionality of a modified nucleotide containing an alkynelinkage and representative electrophoretic gels A, B, and C.

FIG. 5 shows functionality of a modified nucleotide containing an alkenelinkage.

FIG. 6 shows functionality of a modified nucleotide containing an alkanelinkage.

FIG. 7 shows functionality of a modified nucleotide containing an alkanelinkage.

FIG. 8 shows functionality of a modified nucleotide containing an alkanelinkage.

FIG. 9 schematically shows enrichment of RNA binding proteins usinglabeled RNA as bait.

FIG. 10 shows synthesis of azide-(poly)ethylene glycol(PEG)_((n))-alkane cytidine intermediate.

FIG. 11 shows synthesis of R-PEG_((n))-alkane-3′5′-bisphosphatecytidine.

FIG. 12 shows two RNA pull-down labeling reagents.

FIG. 13 shows RNA binding protein enrichment using overexpressionlysate.

FIG. 14 shows RNA binding protein enrichment using cell lysate.

FIG. 15 shows RNA binding protein enrichment using endogenous lysate anddesthiobiotin-PEG₄-alkane-3′5′-bisphosphate cytidine.

FIG. 16 shows RNA binding protein enrichment using overexpression lysateand biotin-PEG₁₂-alkane-3′5′-bisphosphate cytidine.

FIG. 17 shows RNA binding protein enrichment using crosslinking andbiotin-PEG₁₂-alkane-3′5′-bisphosphate cytidine.

As subsequently disclosed, the nucleotide can be modified by adding atleast one of the following substituents that function as detectormolecules, either directly or indirectly: biotin and derivatives, azide,alkyne, aldehyde, diene, amine, disulfide, fluorophore, spin label,polyethyleneglycol (PEG). These substituents are added in variouspermutations, specific entities, and chain lengths.

In one embodiment, the modified nucleotide is a biotinylated nucleotidehaving the formula biotin-polyethylene glycol (PEG)-alkane-nucleotidewith PEG having at least 7 carbon atoms and up to 100 carbon atoms. Forany of the disclosed inventive compounds, the compound includes the saltform, conjugate base, tautomer, and/or ionized form. In one embodiment,the modified nucleotide is a ribonucleotide. In one embodiment, theribonucleotide can be, but is not limited to, cytidine.

In one embodiment, the biotinylated nucleotide is a cytidine3′-5′-bisphosphate having a PEG₄ linker with the structure shown below.

This structure had enhanced ligation efficiency over prior artbiotinylated compounds due to the presence of the alkane adjacent tocytidine.

One embodiment is a method for labeling an RNA probe with a biotinylatednucleotide having the structure

under conditions that label the RNA probe. The modified ribonucleotideis incubated with an enzyme capable of ligating the biotinylatedribonucleotide to the RNA probe (e.g., a ligase such as T4 ligase), toresult in a biotin-labeled RNA probe. In one embodiment, single strandedT4 ligase is used. In one embodiment, double stranded T4 ligase is used.In one embodiment, thermostable T4 ligase is used. Examples of suitableligases include T4 RNA Ligase 1 (applications include labeling of3′-termini of RNA with 5′-[³²P] pCp, inter- and intramolecular joiningof RNA and DNA molecules; synthesis of single-strandedoligodeoxyribonucleotides; and incorporation of unnatural amino acidsinto proteins); T4 RNA Ligase 2 (applications include ligating a nick indsRNA, splintered RNA ligation, and ligating the 3′ OH of RNA to the 5′phosphate of DNA in a double stranded structure); T4 RNA Ligase 2,truncated (applications include joining a single stranded adenylatedprimer to RNAs for cloning, and small RNA cloning); T4 RNA Ligase 2,truncated K227Q (applications include joining a single strandedadenylated primer to RNAs for cloning, small RNA cloning, and ligatingwith the lowest possible ligation byproduct); each of which iscommercially available from New England BioLab; and thermostable RNAligase, which is able to perform ligations at elevated temperatures,such as above about 40°, commercially available from Epicentre. In oneembodiment, the modified nucleotide is purified prior to ligation.Subsequent assaying for the biotinylated probe permits detection of thepresence, quantity, etc. of the ribonucleotide in the sample. The methodis used with, e.g., and without limitation, mobility shift assays,Northern blots, in situ hybridization, etc. Biotin-labeled RNA probe canbe detected using a streptavidin-conjugated reporter molecule such as,e.g. and without limitation, enzymes (e.g., peroxidases), fluorescentdyes, etc.

One embodiment is a method of synthesizingbiotin-PEG-4-alkane-3′,5′-cytidine-bisphosphate.

One embodiment is a kit containing a compound having the structure

and instructions for labeling a nucleic acid using the compound. The kitcan also contain an enzyme, a control RNA (either labeled or unlabeledwith the modified nucleotide), and buffer.

The modified nucleotide has enhanced ligation efficiency over knowncompounds due to the presence of an alkane linkage. The alkane linkagealso improves functionality of the modified nucleotide by decreasingreactivity of the modified nucleotide with cell lysates. The PEG spacerincreases hydrophilicity of the modified nucleotide to increaseaccessibility of the biotin for detection.

In one embodiment, the biotinylated nucleotide compounds have thefollowing structure: P1-P2-Nus-Alk-Lnk-Obs (I) or its salt, conjugatebase, tautomer, or ionized form where

P1 and P2 are phosphate groups;

Nus is a nucleoside (a sugar (e.g., ribose) bound to a purine orpyrimidine base);

Alk is a connecting group that can be directly or indirectly bondedbetween Nus and Lnk, having the structure -//—(CH₂)_(m)—Y—//- in which Yis a bond forming group selected from

and m is an integer ranging from 3 to 6 inclusive, and the leftmost bondis to Nus and the rightmost bond is to Lnk;

Lnk is a linking group between Alk and Obs, having the followingstructures

in which n is an integer ranging from 2 to 48 inclusive;

-   -   A₁ is a bond forming group selected from

-   -   A₂ is a bond forming group selected from

-   -   A₃ is a bond forming group selected from

X is a cleavable group that can undergo silicon-carbon cleavage,nucleophilic cleavage, redox cleavage, photochemical cleavage, enzymaticcleavage, or exchange-based cleavage; and

Obs is an observable label.

Y functions as a handle to permit attachment of detector molecules(e.g., fluorophore, biotin, etc.)

When the sugar is ribose, it has the following attachments: P1 isattached at the 5′ position; P2 is attached at the 3′ position; and thepurine or pyrimidine base is attached at the 1′ position.

The purine or pyrimidine base is selected from cytosine (C), uracil (U),adenine (A), thymine (T), guanine (G), or inosine (I) and may bemodified or unmodified. Embodiments include, but are not limited to,1-methyladenine, N6-methyladenine, N6-isopentyladenine,N,N-dimethyladenine, 7-deazaadenine, 2-thiocytosine, 3-methylcytosine,N4-acetylcytosine, 2-thiocytosine, 1-methylguanine, 2-methylguanine,7-methylguanine, N2,N2-dimethylguanine, 7-deazaguanine, 2-thiouracil,6-thiopurine, or 2,6-diaminopurine.

The modification may be an observable label. Observable labels include,but are not limited to, a chromogenic moiety, a fluorophore such asfluorescein, rhodamine, a commercial dye (e.g., DyLight® (Dyomics),Alexa®, Cy3, Cy5), a mass label, a spin label, or a moiety capable ofbinding an observable label, such as a streptavidin-binding label suchas biotin, desthiobiotin or iminobiotin, or a secondary detection labelsuch as azide, alkyne, aldehyde, or diene, which are capable of forminga covalent bond with an alkyne, phosphine, azide, hydrazide,alkoxyamine, or alkene present on an observable label. In oneembodiment, the observable label is biotin, and the compound isbiotin-PEG₄-alkane-3′,5′-cytidine-bisphosphate. In one embodiment, theobservable label is an azide, and the compound isazido-PEG₄-alkane-3′,5′-cytidine-bisphosphate. In one embodiment, theobservable label is a fluorophore, and the compound isCy5-PEG₄-alkane-3′,5′-cytidine-bisphosphate. Labeling occurs with highefficiency and comparable sensitivity to radioisotope labeling, yetavoids the use of radioactivity with its concomitant disadvantages.

In one embodiment, n is an integer ranging from 2 to 24 inclusive, thesugar is ribose, the purine or pyrimidine base is A, C, G, U, or I, m is3, n is 4, and the observable label is a streptavidin-binding labelselected from biotin, desthiobiotin, or iminobiotin.

In one embodiment, the modified nucleotide compounds have the followingstructure (II):

or its salt, conjugate base, tautomer, or ionized form where

Base* is a purine or pyrimidine base;

R is H, OH, CH₃, or a hydroxyl protecting group;

Alk is a connecting group between Base* and Lnk, having the structure-//—(CH₂)_(m)—Y—//- in which Y is a bond forming group selected from

andm is an integer ranging from 3 to 6 inclusive;

Lnk is a linking group having the following structures:

in which n is an integer ranging from 2 to 48 inclusive;

A₁ is a bond forming group selected from

A₂ is a bond forming group selected from

A₃ is a bond forming group selected from

X is a cleavable group that can undergo silicon-carbon cleavage,nucleophilic cleavage, redox cleavage, acid cleavage, base cleavage,photochemical cleavage, enzymatic cleavage, or exchange-based cleavage;

Obs is an observable label moiety.

The sugar group may be ribose or deoxyribose. The purine or pyrimidinebase is selected from C, U, A, G, T, or I and may be modified orunmodified. Embodiments include, but are not limited to,1-methyladenine, N6-methyladenine, N6-isopentyladenine,N,N-dimethyladenine, 7-deazaadenine, 2-thiocytosine, 3-methylcytosine,N4-acetylcytosine, 2-thiocytosine, 1-methylguanine, 2-methylguanine,7-methylguanine, N2,N2-dimethylguanine, 7-deazaguanine, 2-thiouracil,6-thiopurine, or 2,6-diaminopurine.

The observable label may be a chromogenic moiety, a fluorophore such asfluorescein, rhodamine, a commercial dye (e.g., DyLight® (Dyomics),Alexa®, Cy3, Cy5), a mass label, a spin label, or a moiety capable ofbinding an observable label, such as a streptavidin-binding label suchas biotin, desthiobiotin or iminobiotin, or a secondary detection labelsuch as azide, alkyne, aldehyde, or diene.

In one embodiment, n is an integer ranging from 2 to 24 inclusive. Inone embodiment, the sugar is ribose, the purine or pyrimidine base is A,C, G, U, or I, m is 3, n is 4, and the observable label is astreptavidin-binding label selected from biotin, desthiobiotin, oriminobiotin.

In one embodiment, the sugar is ribose, the purine or pyrimidine base isC, m is 3, Lnk is

n is 4, A₁ is

A₂ is

and when present, A₃ is

and Obs is selected from the group consisting of biotin, a fluorophore,and an azide.

One embodiment is a method of labeling RNA by heating the desired RNAsample to at least 75° C. up to 95° C. In one embodiment, the solutioncontaining the RNA sample contained dimethylsulfoxide (DMSO) at aconcentration ranging from 0% to 25%. The RNA sample was heated for 1minute to 5 minutes, then rapidly cooled on ice to between 2° C. and 10°C. for at least one minute. The RNA then was contacted with one of themodified nucleotide compounds having the structure P1-P2-Nus-Alk-Lnk-Obsas described above. The nucleotide was ligated to the RNA to result in alabeled RNA.

The modified nucleotide was ligated to the RNA using an enzyme such as,but not limited to, T4 RNA ligase, to result in a labeled RNA. In thisembodiment, RNA was heated to at least 75° C., and up to 95° C., thencooled for at least one minute to less than 10° C. The cooled RNA wasthen contacted with the biotinylated cytidine bisphosphate underreaction conditions using T4 RNA ligase and including PEG havingmolecular weight between about 1500 and 24,000 inclusive and at aconcentration ranging from 5% PEG to 20% PEG inclusive. The reaction wasincubated between 30 minutes and 16 hours at temperature ranging between16° C. and 37° C. to ligate the biotinylated cytidine bisphosphate tothe RNA, resulting in a modified RNA.

Synthesis of exemplary specific compounds among each of the followingmodified nucleotides is subsequently described. One skilled in the artwill appreciate that such synthesis schemes are representative and notlimiting; one skilled in the art will know how to synthesize otherspecific examples using known methods and without undue experimentation.They include, but are not limited to: biotin-PEG₄ modifications:overview of biotin-PEG₄-alkane-3′,5′-cytidine-bisphosphate(BPA-3′,5′-pCp, compound 6), overview ofbiotin-PEG₄-SS-alkane-3′,5′-cytidine-bisphosphate (BP₄SSA-3′,5′-pCp,compound 12), biotin-PEG₄-SS-alkane-cytidine (BP₄SSAC, compound 11), anddetailed reactions for biotin-PEG₄-SS-alkane-3′,5′-cytidine-bisphosphate(BP₄SSA-3′,5′-pCp, compound 12); biotin-PEG₁₂ modifications; azido-PEG₄modifications; fluorophore-PEG₄ modifications, DyLight550-PEG₄-alkane-3′,5′-cytidine-bisphosphate (Dy550P₄A-3′,5′-pCp,compound 14).

Biotin-PEG₄ Modification

One embodiment is a method of preparing biotin-polyethylene glycol(PEG)-alkane-3′,5′-cytidine-bisphosphate. The method reacts propargylamine with methyl trifluoroacetate to result inpropargyltrifluoroacetamide. The propargyltrifluoroacetamide reacts with5-iodocytidine to result in 5-[3-(trifluoroacetamido)propynyl]cytidine.The 5-[3-(trifluoroacetamido)propynyl]cytidine then is converted to5-[3-(trifluoroacetamido)propyl]cytidine. The5-[3-(trifluoroacetamido)propyl]cytidine then is converted to5-(3-aminopropyl)cytidine. The 5-(3-aminopropyl)cytidine then is reactedwith NHS-PEG-biotin to result in biotin-PEG-alkane-cytidine. Thebiotin-PEG-alkane-cytidine then is reacted with diphosphoryl chloride toresult in biotin-polyethylene glycol(PEG)-alkane-3′,5′-cytidine-bisphosphate.

Proparglytrifluoroacetamide (1) was prepared according to the followingreaction:

Propargyl amine (4.00 g, 72.62 mmol, 1.00 equiv.) was added dropwise tomethyl trifluoroacetate (11.16 g, 87.15 mmol, 1.20 equiv.) at 0° C. Thereaction mixture was stirred at 0° C. for 2 h and then concentratedunder reduced pressure to remove methanol. The product was purified byvacuum distillation yielding propargyltrifluoroacetamide as a colorlessliquid (9.59 g, 87%). The structure was confirmed by ¹H- and ¹⁹F-NMR.

5-[3-(trifluoroacetamido)propynyl]cytidine (2) was prepared according tothe following reaction:

A 100-mL three-necked flask was charged with 5-iodocytidine (2.66 g,7.00 mmol, 1.00 equiv.), cuprous iodide (0.267 g, 1.40 mmol, 0.20equiv.) and dry DMF (35 mL). After complete dissolution of the reactionmixture, propargyltrifluoroacetamide (3.17 g, 21.00 mmol, 3.00 equiv.),triethylamine (1.42 g, 14.00 mmol, 2.00 equiv.) and finally tetrakis(triphenylphosphine)palladium(0) (0.809 g, 0.70 mmol, 0.10 equiv.) wereadded to the reaction mixture under N₂. The reaction was stirred atambient temperature (around 19° C. to around 22° C.) under N₂ for 18-24h. The reaction was then diluted with 70 mL of 1:1methanol-dichloromethane and the bicarbonate form of AGI X8 resin (12.00g) was added. After stirring for about one h, the reaction mixture wasfiltered and the resin was washed with 1:1 methanol-dichloromethane. Thecombined filtrates were rapidly concentrated with a rotary evaporator.The residue was immediately purified by flash chromatography. Removal ofsolvent from the appropriate fractions afforded 1.84 g (67%) of5-[3-(trifluoroacetamido)propynyl]cytidine as a light brown solid, whichwas confirmed by ¹H-NMR.

5-[3-(trifluoroacetamido)propyl]cytidine (3) was prepared according tothe following reaction:

5-[3-(trifluoroacetamido)propynyl]cytidine (1.25 g, 3.19 mmol, 1.00equiv.) was dissolved in methanol (30 mL). Palladium hydroxide (0.25 g,20 wt./wt. % based on propynyl cytidine) and triethylsilane (3.71 g,31.90 mmol, 10.00 equiv.) were added to the reaction mixture. After20-24 hours at ambient temperature, the reaction mixture was filteredthrough glass fiber and the filtrate was concentrated under reducedpressure giving a dark brown residue. The residue was purified by flashchromatography. Removal of solvent from the appropriate fractionsafforded 0.85 g (71%) of 5-[3-(trifluoroacetamido)propyl]cytidine as acream colored solid, which was confirmed by ¹H-NM.

5-(3-aminopropyl)cytidine (4) was prepared according to the followingreaction:

5-[3-(trifluoroacetamido)propyl]cytidine (0.69 g, 1.74 mmol) wasdissolved in DI H₂O (8.5 mL). After complete dissolution, concentratedammonium hydroxide (NH₄OH) (8.5 mL) was added to the reaction mixture.The reaction solution was stirred at ambient temperature for 2-3 h andthen concentrated under reduced pressure giving the crude product asyellow-orange residue. The crude product was dissolved in deionized H₂O(10 mL) and AG50W-X8 resin (2.5 g) was added to the solution. Thesuspension was stirred for 15 min and filtered over a bed of AG50W-X8resin (2.5 g). The resin was washed with DI H₂O and the product was theneluted off of the resin by washing the resin with deionized H₂O/conc.NH₄OH, 4:1, collecting fractions (monitored by TLC). Removal of solventfrom the appropriate fractions afforded 0.51 g (98%) of5-(3-aminopropyl)cytidine as light tan solid, which was confirmed by¹H-NMR.

Biotin-PEG₄-alkane-cytidine (BPAC, 5) was prepared according to thefollowing reaction:

NHS-PEG₄-biotin (0.196 g, 0.333 mmol, 1.00 equiv.) was dissolved in DMF(10 mL). 5-(3-aminopropyl)cytidine) (0.100 g, 0.333 mmol, 1.00 equiv.)was added to the reaction solution. The reaction solution was stirred atambient temperature under N₂ atmosphere. After 20-24 h, the reactionmixture was concentrated under reduced pressure giving the crudeproduct. The crude product was purified by flash chromatography. Removalof solvent from the appropriate fractions afforded 0.18 g (69%) of BPACas a white solid, which was confirmed by ¹H-NMR.

Biotin-PEG₄-alkane-3′,5′-cytidine-bisphosphate (BPA-3′,5′-pCp, 6) wasprepared according to the following reaction:

BPAC (0.061 g, 0.079 mmol, 1.00 equiv.) was partially dissolved indiphosphoryl chloride (196 μL, 1.66 mmol, 21.00 equiv.), previouslycooled to −10° C. to −15° C. in a 1-mL Reacti-Vial™. The mixture wasthen stirred at −10° C. to −15° C. After 5 h, the reaction was quenchedby addition of ice cold water (1-2 mL) and, immediately thereafter, witha chilled solution of 0.5 M TEAB buffer, pH 8.5 (17 mL). Uponstabilization at neutral pH, the colorless solution was stirred atambient temperature for 30 min and concentrated using a rotaryevaporator until complete removal of TEAB. The solution was desaltedusing a C18 cartridge (Waters) and purified by FPLC (MonoQ 10/100GLcolumn, GE) using a pH gradient. After a final desalting using again aC18 cartridge (Waters), BPA-3′,5′-pCp was isolated after lyophilizationas a white solid (10 mg, 9%), which was confirmed by ¹H-NMR & HPLC.

Overview of Preparation ofBiotin-PEG₄-SS-alkane-3′,5′-cytidine-bisphosphate (BP₄SSA-3′,5′-pCp,Compound 12)

The reaction scheme to prepare biotin-polyethylene glycol(PEG)-SS-alkane-3′,5′-cytidine-bisphosphate is as follows. The5-(3-aminopropyl)cytidine (compound 4) is reacted with NHS-SS-PEG-biotinto result in biotin-PEG-SS-alkane-cytidine (compound 11). Thebiotin-PEG-SS-alkane-cytidine (compound 11) then is reacted withdiphosphoryl chloride to result in biotin-polyethylene glycol(PEG)-SS-alkane-3′,5′-cytidine-bisphosphate (compound 12).

Preparation of Biotin-PEG₄-SS-alkane-cytidine (BP₄SSAC, Compound 11)

NHS-SS-PEG₄-biotin (0.250 g, 0.333 mmol, 1.00 equiv.) was dissolved inDMF (10 mL). 5-(3-aminopropyl)cytidine) (0.100 g, 0.333 mmol, 1.00equiv.) was added to the reaction solution. The reaction solution wasstirred at ambient temperature under N₂ atmosphere. After 20-24 hours,the reaction mixture was concentrated under reduced pressure giving thecrude product. The crude product was purified by flash chromatography.Removal of solvent from the appropriate fractions afforded 0.19 g (61%)of BP₄SSAC (compound 11) as a white solid, which was confirmed by¹H-NMR.

Preparation of Biotin-PEG₄-SS-alkane-3′,5′-cytidine-bisphosphate(BP₄SSA-3′,5′-pCp, Compound 12)

BP₄SSAC (0.074 g, 0.079 mmol, 1.00 equiv.) was partially dissolved indiphosphoryl chloride (196 μL, 1.66 mmol, 21.00 equiv.), previouslycooled to −10° C. to −15° C. in a 1-mL Reacti-Vial™. The mixture wasthen stirred at −10° C. to −15° C. After five hours, the reaction wasquenched by addition of ice cold water (1-2 mL) and, immediatelythereafter, with a chilled solution of 0.5M TEAB buffer, pH 8.5 (17 mL).Upon stabilization at neutral pH, the colorless solution was stirred atambient temperature for 30 min and concentrated using a rotaryevaporator until complete removal of TEAB. The solution was desaltedusing a C18 cartridge (Waters) and purified by FPLC (MonoQ 10/100GLcolumn, GE) using a pH gradient. After a final desalting using again aC18 cartridge (Waters), BP₄SSA-3′,5′-pCp (compound 12) was isolatedafter lyophilization as a white solid (5 mg, 6%), which was confirmed by¹H-NMR and HPLC.

Biotin-PEG₁₂ Modification Preparation of Biotin-PEG₁₂-alkane-cytidine(BP₁₂AC, Compound 7)

NHS-PEG₁₂-biotin (0.313 g, 0.333 mmol, 1.00 equiv.) was dissolved in DMF(10 mL). 5-(3-aminopropyl)cytidine) (0.100 g, 0.333 mmol, 1.00 equiv.,compound 4) was added to the reaction solution. The reaction solutionwas stirred at ambient temperature under N₂ atmosphere. After 20-24 h,the reaction mixture was concentrated under reduced pressure giving thecrude product. The crude product was purified by flash chromatography.Removal of solvent from the appropriate fractions afforded 0.27 g (72%)of BP₁₂AC (compound 7) as a light yellow foam, which was confirmed by¹H-NMR.

Preparation of Biotin-PEG₁₂-Alkane-3′,5′-bisphosphate-cytidine(BP₁₂A-3′,5′-pCp, Compound 8)

Biotin-PEG₁₂-alkane-cytidine (0.135 g, 0.120 mmol, 1.00 equiv., compound7) was partially dissolved in diphosphoryl chloride (315 μL, 2.40 mmol,20.00 equiv.), previously cooled to −10 to −15° C. in a 1-mLReacti-Vial™. The mixture was stirred at −10 to −15° C. After fivehours, the reaction was quenched by adding ice cold water (1-2 mL) andimmediately after with a chilled solution of 0.5M TEAB buffer, pH 8.5(40 mL). Upon stabilization at neutral pH, the colorless solution wasstirred at ambient temperature for 30 min and concentrated using arotary evaporator until TEAB was completely removed. The solution wasdesalted using a C18 cartridge (Waters) and purified by FPLC (MonoQ10/100GL column, GE) using a pH gradient. After final desalting using aC18 cartridge (Waters), biotin-PEG₁₂-alkane-3′,5′-cytidine-bisphosphate(compound 8) was isolated after lyophilization as a sticky white solid(8 mg, 5%), which was confirmed by 1H-NMR and HPLC.

Azido-PEG₄ Modification Azido-PEG₄-alkane-3′,5′-cytidine-biphosphate,Compound 9

One embodiment is a method of preparingazido-PEG₄-alkane-3′,5′-cytidine-bisphosphate. The5-(3-aminopropyl)cytidine was synthesized as described above, then wasreacted with NHS-PEG₄-azide to result in azido-PEG₄-alkane-cytidine. Theazido-PEG₄-alkane-cytidine was then reacted with diphosphoryl chlorideto result in azido-PEG₄-alkane-3′,5′-cytidine-bisphosphate.

NHS-PEG₄-azide (0.408 g, 1.05 mmol, 1.00 equiv.) was dissolved in DMF(32 mL). The 5-(3-aminopropyl)cytidine) (0.315 g, 1.05 mmol, 1.00equiv.) was added to the reaction solution. The reaction solution wasstirred at ambient temperature under N₂ atmosphere. After 20-24 hours,the reaction mixture was concentrated under reduced pressure giving thecrude product. The crude product was purified by flash chromatography.Removal of solvent from the appropriate fractions afforded 0.378 g (63%)of azido-PEG₄-alkane-cytidine (compound 9) as a near colorless glass,which was confirmed by 1H-NMR.

Azido-PEG₄-alkane-3′,5′-Bisphosphate-Cytidine (AzP₄A-3′,5′p-C-p),Compound 10

Azido-PEG₄-alkane-cytidine (0.150 g, 0.262 mmol, 1.00 equiv., compound9) was partially dissolved in diphosphoryl chloride (688 μL, 5.24 mmol,20.00 equiv.), previously cooled to −10 to −15° C. in a 1 mLReacti-Vial™. The mixture was then stirred at −10 to −15° C. After fivehours, the reaction was quenched by adding ice cold water (2-3 mL) andthen immediately with a chilled solution of 0.5M TEAB buffer, pH 8.5 (87mL). Upon stabilization at neutral pH, the colorless solution wasstirred at ambient temperature for 30 min and concentrated using arotary evaporator until TEAB was complete removed. The solution wasdesalted using a C18 cartridge (Waters) and purified by FPLC (MonoQ10/100GL column, GE) using a pH gradient. After final desalting usingagain a C18 cartridge (Waters),azido-PEG₄-alkane-3′,5′-cytidine-bisphosphate (compound 10) was isolatedafter lyophilization as a sticky white solid (10 mg, 6%), confirmed by1H-NMR and HPLC.

Fluorophore-PEG₄ Modifications Overview—Preparation of DyLight550-PEG₄-alkane-3′,5′-cytidine-bisphosphate (Dy550P₃A-3′,5′-pCp, 14)

DyLight 550-polyethylene glycol (PEG)-alkane-3′,5′-cytidine-bisphosphate(compound 14) is prepared as follows. Theazido-PEG₄-alkane-3′,5′-cytidine-bisphosphate (compound 10) wassynthesized as described above, then allowed to react withtris(2-carboxyethyl)phosphine hydrochloride (TCEP) to result inamino-PEG₄-alkane-3,′5′-cytidine bisphosphate (compound 13). Theamino-PEG₄-alkane-3,′5′-cytidine bisphosphate (compound 13) was thenreacted with DyLight 550 NHS ester to result in 550-polyethylene glycol(PEG)-alkane-3′,5′-cytidine-bisphosphate (compound 14).

Preparation of Amino-PEG₄-alkane-3′,5′-bisphosphate-cytidine(AmP₄A-3′,5′-pCp, 13

Azido-PEG₄-alkane-3′,5′-bisphosphate-cytidine (3.56 μmol, 1.00 equiv.,compound 10) was dissolved in 200 mM Tris/HCl, pH 7.5 (800 μL).Tris(2-carboxyethyl)phosphine hydrochloride (TCEP) (17.54 mg, approx.5.00 equiv.) was dissolved in 200 mM Tris/HCl, pH 7.5 (688 μL). The TCEPsolution (200 μL) was added to the solution of azide and the reactionwas mixed at ambient temperature. After 1-3 h, the reaction mixture waspurified by FPLC and the fractions containing product were treateddirectly with DyLight 550 NHS ester to result inamino-PEG₄-alkane-3′,5′-bisphosphate cytidine (compound 13).

Preparation of DyLight550-PEG₄-alkane-3′,5′-bisphosphate-cytidine(Dy550P₄A-3′,5′-pCp, 14)

The pH of an FPLC fraction (2 mL) containingamino-PEG₄-alkane-3′,5′-bisphosphate-cytidine (compound 13) was adjustedto pH 7.0 by adding 1M HEPES, pH 7.3. Separately, a 1 mM solution ofDyLight 550 NHS ester was prepared by dissolving DyLight 550 NHS ester(MW=1040.05, 1 mg) in ultra pure water (960 μL).Amino-PEG₄-alkane-3′,5′-bisphosphate-cytidine (0.25 mL) and DyLight 550NHS ester (0.25 mL) were combined in a separate reaction vessel and weremixed with rotation for 1 h at ambient temperature. The reaction mixturewas purified by FPLC (MonoQ 10/100GL column, GE) using a pH and saltgradient. Fractions containing product were dialyzed and subsequentlylyophilized, yielding DyLight550-PEG₄-alkane-3′,5′-cytidine-bisphosphate(compound 14) as a dark pink residue.

Other exemplary compounds follow. Examples of fluorescent compoundsinclude, but are not limited to, the following:

Examples of compounds with mass labels include, but are not limited to,the following:

Examples of compounds with a spin label include, but are not limited to,the following:

An example of a desthiobiotin-containing compound is:

Examples of compounds with alternative cleavage include, but are notlimited to, the following:

One embodiment is a kit to label RNA with the compound described above.In one embodiment, the kit contains the compound(s), ligase, ligasebuffer, and labeling instructions. In one embodiment, the kit containsadditional kit components to enhance ligation efficiency includingpolyethylene glycol as a size exclusion reagent and DMSO to relaxsecondary structure. In one embodiment, the kit also includes a controlRNA that ligates with greater than 75% efficiency, and a syntheticbiotinylated RNA control to assess ligation efficiency. Instructionsinclude methods for a typical ligation reaction using the reagentslisted and/or instructions for using a nucleic acid comprising thelabeled nucleotide in a method, such as mobility shift, Northern blot,pull-down assay, or in situ hybridization. In one embodiment, the kitcontains a described compound where the sugar is ribose, the purine orpyrimidine base is C, m is 3, Lnk is

n is 4, A₁ is

A₂ is

and when present, A₃ is

and Obs is selected from the group consisting of biotin, a fluorophore,and an azide.

For mobility shift assays, an excess of the labeled RNA was incubatedwith a solution containing the protein, RNA, or DNA of interest in anoptimized binding buffer. The incubation conditions were empiricallydetermined; incubation time typically ranged from 5 minutes to 1 hour,incubation temperatures typically ranged from 4° C. to room temperature(19° C. to 22° C.). The binding reaction was then subjected toelectrophoresis to separate RNA binding complexes from free probe. Theshifted RNA complex was then detected in-gel, or transferred to apositively charged membrane and detected using secondary detectionreagents (i.e., with a chromogen, or by chemiluminescence).

For Northern blotting, the labeled RNA was used for the detection of RNAthat had been separated by electrophoresis and transferred onto amembrane. The labeled RNA was denatured for 5-10 minutes at 95° C. andquickly cooled on ice to less than 10° C. The denatured probe was thenadded to an optimized hybridization solution and incubated with themembrane at an empirically determined temperature for at least 1 hour,but up to overnight. The membrane was then washed and RNA was detectedusing secondary detection reagents (i.e., chromogen, bychemiluminescence).

For an assay using a labeled RNA to enrich for a component, whether thesubstance containing the component was bound to a chip, resin, etc.(e.g., a “pull-down” assay), labeled RNA was incubated in a bindingreaction containing the protein, RNA, or DNA of interest, an optimizedbinding buffer, and affinity resin. The resin was then washed, the RNAcomplex was eluted, and the protein, DNA, or RNA of interest wasdetected using techniques including but not limited to PCR, RT-PCR,Western blot, or microarray.

For in situ hybridization, the labeled RNA is used as a probe for thedetection of the RNA or RNA complex of interest in cells. The labeledRNA may be used after cells have been fixed onto a support (i.e., amicroscope slide, coverslip, tissue dish, microwell, etc.), or insuspension for flow cytometric analysis. Similarly, the labeled RNA maybe transfected into live cells, and detected directly or using secondaryreagents. The RNA or RNA complex is visualized using techniquesincluding but not limited to light or fluorescent microscopy, flowcytometric analysis, or microarray.

In the experiments subsequently described, T4 RNA ligase was used tolabel RNA with biotinylated cytidine 3′,5′ bisphosphate. Severalmolecules were synthesized to optimize the nucleotide for optimalligation efficiency and functionality, for example, preservation of theinteraction of the labeled RNA with other RNA or cellular proteins.Three different alkyl linkages were tested, including alkyne, alkene,and alkane, in combination with both LC (long chain), SC (short chain),and PEG spacers, as shown in FIGS. 1-3. The molecules were tested forligation efficiency and functionality utilizing establishedelectrophoretic mobility shift (EMSA) controls. In a mobility shiftassay, labeled RNA probe is incubated with a cell lysate containing theprotein(s) of interest in a binding reaction. The reaction is thenelectrophoresed on a non-denaturing gel. Unbound probe will migrate tothe bottom of the gel, while protein bound probe will migrate moreslowly, resulting in a bandshift. The alkyne-LC- andalkyne-SC-containing nucleotides ligated with good efficiency; however,the alkyne linkage was reactive in cell lysates. In a purified systemusing an RNA polymerase template and purified RNA polymerase, the alkynecompounds produced a functional gel shift (FIG. 4 A, electrophoreticgel), while the alkyne compound did not produce a functional gel shiftwith the iron responsive element (IRE)-iron responsive protein (IRP)control utilizing cytosolic liver extract (FIG. 4, electrophoretic gelB). When the liver extract was mixed with purified RNA polymerase, thebandshift was affected, suggesting that the alkyne compound is reactivewith liver extract (FIG. 4, electrophoretic gel C). Similar results wereobtained with the alkene compounds, where the IRE-IRP control ligated,but did not produce a functional bandshift (FIG. 5). The nucleotidecontaining the alkane linkage and PEG spacer was the most optimalcompound for both ligation efficiency and functionality (FIG. 6).

Utilizing the biotin-PEG4-alkane 3,5 cytidine bisphosphate molecule,optimal ligation conditions were determined. The conditions describedresulted in ligation efficiencies greater than 70%, and in some casesgreater than 90%, depending upon the RNA secondary structure andligation conditions. A standard reaction had a donor to acceptorligation ratio of greater than 20:1. The reaction buffer contained 20 Uto 40 U T4 RNA ligase, 40 U RNase inhibitor, 50 mM Tris-HCl, 10 mMMgCl₂, 10 mM DTT, 1 mM ATP (pH 7.8 at 25° C.), and 15% polyethyleneglycol (PEG, MW 20,000). To achieve ligation efficiencies greater than70%, reactions were incubated at 37° C. for 30 minutes, or at 16° C.from 30 minutes to 24 hours, depending upon the RNA length and secondarystructure. In one embodiment, reactions contained 25 pmol to 50 pmolRNA, 1 nmol biotinylated nucleotide, and 20 U to 40 units of T4 RNAligase in a 30 μl reaction volume. An excess of biotinylated nucleotidedid not affect ligation efficiencies, and a range 1 pmol RNA to 200 pmolof RNA was tested in the ligation reaction. The concentration of PEGranged from 5% to 20%.

As shown in the table below, the ligation conditions were assessedutilizing several RNA species, ranging in length, complexity, andfunction to demonstrate efficiency of ligation reaction using RNA ofvarying complexity and length. RNA was derived from the 3′ untranslatedregions (UTR) of mRNA 28-42 nucleotides, miRNA (22-80 nucleotides), andcatalytic RNA (451 nucleotides). RNA was derived synthetically, or fromin vitro transcription reactions.

Length Optimal reaction Description RNA source (bases) conditions IRE(iron 5′ or 3′ UTR synthetic 28 2 hrs 16 C. responsive element element)RNA RNA synthetic 42 30 minutes, 37° C. polymerase >1 hr 16° C. templateRNA mir-16-1 mature micro synthetic 22 ON 16° C. RNA TNF ARE 3′ UTRsynthetic 37 2 hrs 16° C. element Let-7 pre-miRNA in vitro ~70 overnight16° C. transcribed hTR catalytic in vitro 451 overnight 16° C. RNAtranscribed COX-76 3′ UTR in vitro ~70 overnight 16° C. ARE elementtranscribed mir-16-1 pre-miRNA in vitro ~70 overnight 16° C. transcribed

Ligation efficiencies were greater than 70% with reactions using 25-50pmol RNA, 1 nmol biotinylated nucleotide, 20-40 U T4 RNA ligase, 40 URNase Inhibitor, 50 mM Tris-HCl, 10 mM MgCl₂, 10 mM DTT, 1 mM ATP (pH7.8 at 25° C.), and 15% PEG (MW 20,000). Ligation efficiencies wereimproved for RNAs with extensive RNA secondary structure or length byheating briefly before the ligation reaction; heating temperaturesranged from 80° C.-90° C. for 1-5 minutes, followed by rapid-cooling onice for at least 1 minute to several hours. In some cases, adding 25%DMSO before heating enhanced ligation efficiency. The order of additionof the reaction components did not matter, except for the PEG, which wasadded last. Several PEG varieties were tested including molecularweights of 1500, 6000, 8500, and 20,000. Although the PEG (MW 20,000)best enhanced ligation efficiency, the other PEG molecules wereacceptable, and other size exclusion molecules would also be acceptable.A PEG concentration of 15% was optimal. Other PEG concentrations couldalso be used, ranging from 5% to 20%.

Ligation efficiencies were assessed using dot blot and quantitative spotdensitometry. A synthetically biotinylated RNA was used as a controlwhere 100% biotinylation was assumed. Labeled RNA from the ligationreaction and the synthetically labeled RNA were first normalized toconcentration, and then serially diluted to determine efficiency. Asmall volume was applied (spotted) onto a positively charged nylonmembrane. The membrane was cross-linked using ultraviolet (UV)radiation. Biotinylated RNA was detected using a streptavidinhorseradish peroxidase (HRP) substrate and chemiluminescent detection.The non-saturating spots, which are spots where the densitometryintensity value was not saturated, were quantitated using densitometry.To determine ligation efficiency, labeled RNA was compared to thecontrol standard to determine efficiency. To determine labelingreproducibility, samples were applied (spotted) in triplicate for two ofthe RNA samples for intra-assay variability, and each ligation with theoptimized conditions was repeated at least three independent times forinterassay variability. To determine labeling integrity, labeled RNA wasseparated by electrophoresis on a gel containing 5% acrylamide/8 M urea(denaturing gel), the RNA was transferred to a nylon membrane and wasdetected using chemiluminescence. The results indicated that the labeledprobes were of high quality, of the correct size, and exhibited eitherminimal degradation or no degradation.

In vitro transcribed RNA was derived through transcription from adigested plasmid containing the sequence of interest flanked by a T7polymerase binding site and restriction enzyme site such that only theRNA of interest is transcribed. In vitro transcribed RNA was alsoderived through transcription of complementary primers containing a T7RNA polymerase binding sequence element. Digested plasmid was purifiedby extraction with phenol:chloroform and ethanol precipitation.Complementary primers were annealed in a reaction containing 25 μM ofeach primer in 10 mM HEPES buffer (pH 7.3). Reactions were incubated at95° C. for ten minutes followed by slow cooling at room temperature forat least ten minutes, followed by incubation on ice. Transcriptionreactions typically contained 500 ng-1 μg DNA, 0.5 mM each of ATP, CTP,UTP, and GTP, 1× transcription buffer, 30 U T7 RNA polymerase, and 40units RNAse inhibitor. Reactions were incubated for 30 minutes to 1 hourat 37° C. DNA was digested for ten minutes with RNAse-free DNAse I at37° C., followed by inactivation with EDTA. RNA was then selectivelyprecipitated with ethanol, and transcript purity was determined byeither agarose or non-denaturing polyacrylamide gel electrophoresis.Precipitated RNA was then quantitated by UV-spectroscopy (absorbance at260 nm/280 nm), and 25 pmol-50 pmol of RNA was used in each ligationreaction.

The functionality of the labeled RNA was determined by assaying a knowninteraction of the RNA to ensure that the 3′-end label minimallydisturbed secondary structure. Functionality of labeled iron responsiveelement (IRE), RNA polymerase template, and let-7 micro RNA wasdetermined by RNA electrophoretic mobility shift assay (EMSA). Theprotein sources included cytosolic liver extract containing ironresponsive element-iron responsive protein (IRE-IRP), lin-28overexpression lysate (let-7-lin28), and purified RNA core polymerase(Epicentre). Dilutions of each RNA (nM) were incubated with the proteinof interest in a 1× binding reaction containing 10 mM HEPES (pH 7.3), 20mM KCl, 1 mM MgCl₂, 1 mM DTT, 2.5-10 μg tRNA, and 5% glycerol for 15-30minutes at room temperature (about 20° C. to about 22° C.). Optimalbinding conditions were achieved for RNA polymerase template bysubstituting tRNA with bovine serum albumin (BSA), and increasing theDTT concentration to 3 mM and the KCl concentration to 40 mM for thelet-7-lin28 interaction. Binding reactions composition were separated byelectrophoresis on native 6% acrylamide DNA retardation gels for one hr,100 V, at either room temperature or 4° C. The RNA was then transferredto a positively charged nylon membrane, cross-linked (UV irradiation),and then detected using chemiluminescence. Three binding reactions wereassessed for each labeled RNA: 1) migration and intensity of the freeprobe that migrated toward the bottom of the gel; 2) intensity of thelabeled RNA with protein, resulting in a bandshift of the RNA-proteincomplex; and 3) the competition reaction of the labeled RNA and theunlabeled RNA with protein (FIG. 6). Each bandshift reaction wasrepeated three times with three independently labeled RNAs. Each of the3 end-labeled probes was able to functionally bind its respectiveproteins and produce a robust bandshift, as shown for RNA template-RNApolymerase interaction (FIG. 6A), IRE-IRP interaction (FIG. 6B), andlet-7-lin28 interaction (FIG. 6C). Each probe was also functional at thenanomolar level, indicating that the 50 pmol labeling reaction wassufficient for EMSA studies.

In one embodiment, biotin or other suitable moiety, known by one skilledin the art, on the labeled nucleotide serves as an affinity handle forisolating RNA:protein complexes. The functionality of a describedbiotin-labeled RNA to serve as an affinity handle for isolating RNAcomplexes (containing RNA, DNA, RNA and DNA, or protein) using anaffinity resin, bead, or sensor chip (e.g., pull-down) was determinedusing streptavidin agarose resin and surface plasmon resonance.

IRE-RNA (SEQ ID NO: 1) was labeled using biotinylated cytidinebisphosphate, and T4 RNA ligase. The IRP protein, which binds IRE RNAsequences, was cloned into a vector containing an HA tag and in vitrotranslated using an human cell-free human in vitrotranscription/translation system. Before incubation with thebiotinylated RNA, the IRP lysate was incubated with streptavidin agaroseresin to reduce non-specific binding, and to remove endogenous biotin.The IRP lysate was then incubated with the labeled IRE, or with anon-specific control RNA (SEQ ID NO: 2) which was 3′-labeled withbiotin, in binding buffer (10 mM HEPES pH 7.3, 20 mM KCl, 1 mM MgCl₂, 1mM DTT, 10% glycerol, 40U RNase inhibitor (RNasin®)) for 30 minutes atroom temperature, and was then cross-linked with UV light (254 nm) for10 minutes on ice. Binding reactions were then washed with PBS and theIRE-IRP complex was eluted from the resin. After separation byelectrophoresis and transfer to a membrane, IRP was detected using mouseanti-HA antibody. The results are shown in FIG. 7. Lane 1 is 5 μl HA-IRPIVT lysate, lane 2 is 25 μl flow-through fraction, lane 3 is 50 μl washfraction, and lane 4 is 25 μl eluted fraction.

The ability of the biotin-labeled RNA to enrich for RNA:proteincomplexes using an immobilized streptavidin sensor chip was examinedusing Biacore™ Surface Plasmon Resonance (SPR). The results are shown inFIG. 8 where the solid line is control mRNA and the dashed line is areference (flow cell 1); and where A=biotinylated RNA template controlloading; B=RNA Pol II injection; C=RNA Pol II bound to control RNA; andD=injection of unlabeled control RNA. Biotin-labeled control RNA wascaptured on a Streptavidin-coated sensor chip followed by injection ofbacterial RNA Polymerase. A binding response of RNA polymerase II wasdetected on the active RNA surface and specificity was confirmed by theloss of binding after injection of non-labeled control RNA. Twenty pmollabeled RNA was diluted into nuclease-free HEPES buffer (pH 7.3),injected at 5 l/min for four minutes, and captured onto a commerciallypurchased streptavidin-coated sensor chip for the Biacore 3000®.Bacterial RNA polymerase (0.1 U/μl) was then injected for two minutes.As shown in FIG. 8, a binding response of RNA polymerase II was detectedon the active RNA surface and specificity was confirmed by loss ofbinding after injecting non-labeled control RNA. Specificity wasdetermined through competition of binding RNA polymerase with a 50-100fold excess of non-labeled RNA polymerase template RNA that was injectedfor four minutes.

One embodiment is a method to assay RNA using an RNA probe labeled withthe compound described above and using the method described above. Thelabeled RNA can be synthesized as described above. The labeled RNA probeis contacted with the sample to be assayed under conditions to permitthe labeled RNA to hybridize with RNA in the sample and to detect thehybridization in an assay, e.g., mobility shift, Northern blot, in situhybridization, pull-down assay, etc. using, e.g., astreptavidin-conjugated reporter molecule such as an enzyme, afluorescent compound, an isotope, a gold particle, etc.

Current enrichment and detection of RNA-protein interactions are limitedby inefficient enrichment and release of the RNA-protein complex withoutdisruption the interaction. Nucleotides modified with at least onemoiety or affinity label, e.g., biotin, enriched for and enhanceddetection of protein interactions. Kits containing such modifiednucleotides, such as labeling kits that attach a label (e.g.,fluorogenic substrate) to a nucleotide of interest and resulting in alabeled nucleotide probe, kits to isolate nucleotide binding proteins,and kits to add a crosslinker or another functionality, are alsodisclosed. Methods of synthesizing such modified nucleotides are alsodisclosed.

Enrichment efficiency was improved using labeled RNA as bait for theRNA-protein complex. In one embodiment, the RNA was 3′-end labeled witha modified cytidine-3′,5′-bisphosphate containing a spacer arm with anaffinity handle using T4 RNA ligase. One affinity handle wasdesthiobiotin. One affinity handle was biotin. Different spacer lengthsand compositions maximized accessibility of the RNA to the protein onceattached to a surface (e.g., bead) without compromising secondarystructure. Enrichment efficiency of the RNA-protein complex was assessedusing RNA:protein interactions known to one skilled in this art,including miRNA:Argonaute 2, poly A RNA:PolyA binding protein, andSNRNPA/U1 RNA. In one embodiment, endogenous RNA binding proteins wereobtained from cell lysates or expressed in human in vitro translatedcell lysates. Non-specific binding was determined by incubation oflysate with beads only, or with an unrelated labeled RNA. Elution withbiotin allowed for more flexibility for further downstream applications,e.g., mass spectrometry. The method enriched for additional proteins inthe binding complex, evidenced by isolation of higher molecular weightcomplexes of miRNA:Argonaute detected by Western blot.

Isolation of RNA protein interactions is limited by the tools used forisolation and the inefficiency associated with the enrichment andelution of the complex. Multiple approaches and tools are necessary tocapture both the protein and RNA in the complexes. Both antibody andlabeled RNA as bait are currently used for enrichment of the RNA bindingprotein complexes. These enrichment procedures have been furthermodified for in vivo use, such as using incorporation of 4-thio-uridinefor in vivo crosslinking before capture of the complex with antibody.

Attachment of the handle or detector to the modified nucleotide using a(poly)ethylene glycol (PEG) spacer was determined to be optimal forminimal interference with the RNA protein interaction and detection(U.S. Published Patent Application No. 2011/0262917). The disclosedmethod and kits further streamlines chemical synthesis of the modifiednucleotide, such that the azide-PEG_((n))-alkane cytidine intermediateserves as an affinity handle, or accommodates the addition of a varietyof handles and detectors after reduction using NHS conjugation. In oneembodiment, the PEG spacer is further modified for additionalapplications.

FIG. 9 shows enrichment of RNA binding proteins using labeled RNA asbait. Tools for isolation of RNA-protein interactions include, in oneembodiment, 3′-end labeling RNA with a modified cytidine using T4 RNAligase. Addition of a single label minimized interference with theRNA-protein complex. Additional labeling kits permits flexibility oflabel choice, and labeling of RNA that cannot be made synthetically.

FIGS. 10, 11, and 12 show synthesis of, respectively,azide-PEG_((n))-alkane cytidine intermediate, synthesis ofR-PEG_((n))-alkane-3′,5′-bisphosphate cytidine, and two RNA pull downlabeling reagents.

Optimization for efficient labeling and capture of the RNA proteincomplex was effecting by labeling synthetic RNA and preparingoverexpression lysates using a human in vitro translation system, asshown in FIG. 13. Synthetic RNA (50 pmol/reaction) was end-labeled usinga twenty=fold excess of biotin-PEG₁₂-alkane-3′,5′-bisphosphate cytidinewith T4 ligase. Labeled RNA was incubated with 0.5 mg of streptavidinmagnetic beads for thirty minutes at room temperature. Beads were thenwashed 2× in 20 mM Tris (pH 7.5). PABPC1-GST and SNRPA1-GST proteinswere expressed using a high yield cell-free human in vitro translationsystem. Lysates were diluted 1:10 in binding buffer before use. For thebinding reaction, proteins were incubated with RNA-containing beads(both positive and negative controls), or base beads in 1× bindingbuffer (PABPC1-10 mM Tris (pH 7.5), 2.5 mM MgCl₂, 1-mM KCl, 15%glycerol, 0.5% Tween-20, 10 μg tRNA; SNRPA1-10 mM Tris (pH 7.5), 250 mMNaCl, 1 mM EDTA, 0.5% Tween-20, and 10 μg tRNA) for one hour at 4° C.Beads were washed 3× in 20 mM Tris (pH 7.5), 10 mM NaCl, 0.5 Tween-20.Complexes were eluted using 2× reducing sample buffer. Normalizedsamples were separated by electrophoresis, transferred, and detectedusing PABPC1, GST (SNRPA1) antibodies (1:10000 dilution in TBST-0.5%BSA). Exposure time—1 minute. FT—flow through; 1, 2, 3—washes, Eelution. Expression vector and RNA sequences are indicated in FIG. 13.

RNA was labeled with biotin and desthiobiotin. Non-limiting examplesinclude Poly(A) RNA and U1 RNA with Poly(A) binding protein and SNRPA1,respectively, and Poly(A) binding protein using endogenous HEK 293lysate. Capture using end-labeled RNA effectively captured RNA bindingproteins.

In one embodiment, the disclosed modified nucleotides label an RNAmolecule to result in a labeled RNA probe. The labeled RNA probe is thenused, e.g., in pull-down assays to isolate RNA-complexes containing RNA,DNA, RNA and DNA, and/or protein e.g., RNA-binding proteins.

In contrast to the disclosed method, previous methods to isolateRNA/RNA-binding protein complexes have used either the protein componentof the complex or the DNA component of the complex, instead of the RNAcomponent of the complex, as the capturing moiety or bait. As oneexample, U.S. Pat. Nos. 6,635,422 and 7,504,210 disclose use of proteins(antibodies to the RNA-binding protein of the RNA/protein complex) toisolate endogenously formed complexes. Subsequently, the complexed RNAwas identified and used to create a gene expression profile of mRNA. Asanother example, WO 01/73115 uses double stranded DNA (dsDNA) as bait toisolate transcription factors and investigate modulators oftranscription factor binding.

In contrast to methods using protein or DNA, the disclosed methods use amodified nucleotide that is a single-stranded labeled RNA as bait invarious methods, e.g., to isolate RNA-binding proteins.

In one embodiment, the modified nucleotides have the following generalstructure (I):

The composition can include a salt, conjugate base, tautomer, or ionizedform. P1 is a phosphate group. P2 is a phosphate group. Nus is anucleoside moiety containing a sugar bound to a purine or pyrimidinebase. Alk is a connecting group having the structure -//—(CH₂)_(m)—Y—//-where Y is a bond or bond forming group selected from

and m is an integer ranging from 3 to 6 inclusive; as shown, theleftmost bond in Alk is to Nus, the rightmost bond in Alk is to Lnk. Lnkis a linking group having the structure

where n is an integer ranging from 2 to 48 inclusive; A₁ is a bondforming group selected from

A₂ is a bond forming group selected from

A₃, when present, is a bond forming group selected from

X is a cleavable group that can undergo silicon-carbon cleavage,nucleophilic cleavage, redox cleavage, photochemical cleavage, enzymaticcleavage, or exchange-based cleavage; Z is a branching group thatcontains modifying molecule (Mod); Mod is a modifier or modifyingmolecule (e.g., a crosslinking agent); Obs is an observable label moiety(e.g., an observable label in itself such as a chromogen or fluor, or amolecule that can be rendered observable, a detecting agent; etc.); andthe leftmost bond is to Alk and the rightmost bond is to Mod.

Such modified nucleotides, also termed nucleotide analogs, retainbiological activity. For example, they are substrates for a variety ofDNA and/or RNA polymerases. The modified nucleotide is added to anoligonucleotide or nucleic acid by routine methods, e.g., nicktranslation, random priming, polymerase chain reaction (PCR), 3′-endlabeling, transcribing RNA using SP6, T3, or T7 RNA polymerases, etc.

Modified nucleotides are used to generate labeled probes that may beused in a variety of methods and applications, e.g., biologicalscreening, diagnosis, etc. As one example of use in biologicalscreening, screening an array permits different constituents in acomplex sample to be determined. For example, an oligonucleotide probecontaining a biotinylated nucleotide specifically binds to analytes inthe sample that contain a complementary component, e.g., a nucleic acidor a protein. This yields an observable binding pattern that isdetectable upon interrogating the array. When the complementarycomponent is a protein, the protein may bind and/or associate with thelabeled probe containing a disclosed modified nucleotide. As anotherexample, an oligonucleotide probe or RNA molecule containing a disclosedbiotinylated nucleotide can be used to investigate interactions betweenthe oligonucleotide probe or RNA molecule with RNA-binding proteins,e.g., using the labeled oligonucleotide probe or RNA molecule as bait tocapture RNA-binding proteins in a pull-down assay. In one embodiment,elution of the captured protein(s) and/or complex is accomplished by asoft-release, in which the analyte is eluted under mild conditions,e.g., under non-denaturing conditions, at physiological pH, and/or inthe absence of detergent. In one embodiment, elution is accomplished bycompetitive elution where a component or derivative of a binding moietyis added to compete with the capturing agent, for example, by addingbiotin to competitively elute a biotin-streptavidin captured complex.

A nucleotide is modified by adding at least one of the followingobservable label which function as detector and/or capture molecules andderivatives and variant of the moieties, and adding them either directlyor indirectly: biotin, desthiobiotin, azide, alkyne, aldehyde, diene,amine, hydrazide, disulfide, fluorophore, spin label, mass tag, etc.known to one skilled in the art. These observable labels, either aloneor in combination, are added in various permutations, specific entities,chain lengths, etc. In embodiments, the modified nucleotide contains apolyethylene glycol group (PEG group, also termed a PEG spacer) havingthe structure —(CH₂—O—CH₂)_(n)—, where n is an integer from 2 to 48inclusive. For example, when the modified nucleotide contains fourethylene glycol groups, it is denoted as PEG₄ (i.e., n=4).

In one embodiment, the modified nucleotide is biotinylated and has thestructure

with PEG having at least 7 carbon atoms and up to 100 carbon atoms,i.e., PEG₄ to PEG₅₀. In one embodiment, the modified nucleotide is adesthiobiotinylated nucleotide having the formula

In one embodiment, the modified nucleotide is a mass tagged nucleotidehaving the formula

For any of the disclosed inventive compounds, the compound includes thesalt form, conjugate base, tautomer, and/or ionized form. In oneembodiment, the modified nucleotide is a ribonucleotide. In oneembodiment, the ribonucleotide is cytidine. In one embodiment, theribonucleotide is adenosine. In one embodiment, the ribonucleotide isuridine. In one embodiment, the ribonucleotide is guanosine. In oneembodiment, the ribonucleotide is inosine.

The disclosed modified nucleotide exhibited enhanced ligation efficiencyto a nucleic acid over known compounds due to the presence of an alkanelinkage. As used herein, a nucleic acid refers to a RNA oligonucleotide,an RNA polynucleotide, a DNA oligonucleotide, or a DNA polynucleotide.The alkane linkage also improved functionality of the modifiednucleotide by decreasing reactivity of the modified nucleotide with celllysates. The PEG spacer increased hydrophilicity of the modifiednucleotide to increase accessibility of the biotin for detection and/orcapture.

In embodiments that include a crosslinking molecule, the crosslinkingmolecule is incorporated by incorporation of a branching group Z.

With either ribose or deoxyribose as the sugar, P1 is attached at the 5′position; P2 is attached at the 3′ position; and the purine orpyrimidine base is attached at the 1′ position.

The purine or pyrimidine base is selected from cytosine (C), uracil (U),adenine (A), thymine (T), guanine (G), or inosine (I) and may bemodified or unmodified. Embodiments include, but are not limited to,1-methyladenine, N⁶-methyladenine, N⁶-isopentyladenine,N,N-dimethyladenine, 7-deazaadenine, 2-thiocytosine, 3-methylcytosine,N⁴-acetylcytosine, 2-thiocytosine, 1-methylguanine, 2-methylguanine,7-methylguanine, N₂,N₂-dimethylguanine, 7-deazaguanine, 2-thiouracil,6-thiopurine, or 2,6-diaminopurine.

In one embodiment, the observable label such as a chromogenic moiety, afluorophore such as fluorescein, rhodamine, a commercial dye (e.g.,DyLight® (Dyomics), Alexa®, Cy3, Cy5), a mass tag, such as a commercialmass tag (e.g., Thermo Fisher Tandem Mass Tag (TMT)), a spin label, or amoiety capable of binding an observable label. In one embodiment, theobservable label is a molecule capable of binding or being captured by acorresponding binding partner, such as a streptavidin-binding label suchas biotin, desthiobiotin or iminobiotin, or an antibody. In oneembodiment, the observable label is a secondary detection label such asazide, alkyne, aldehyde, amine, hydrazide, or diene, that is capable offorming a covalent bond with an alkyne, phosphine, azide, hydrazide,alkoxyamine, or alkene present on, e.g., an observable label. In oneembodiment, the modifying molecule, if present, is a crosslinking agent,such as a photoactivatable crosslinking agent, and is capable ofcovalently attaching the modified nucleotide, and a nucleic acid inwhich the modified nucleotide has been incorporated, to anothermolecule.

In one embodiment, the observable label is desthiobiotin, and thecompound is desthiobiotin-PEG₁₂-alkane-3′,5′-cytidine-bisphosphate. Inone embodiment, the observable label is an azide, and the compound isazido-PEG₁₂-alkane-3′,5′-cytidine-bisphosphate. In one embodiment, theobservable label is the mass tag TMT, and the compound isTMT-PEG₁₂-alkane-3′,5′-cytidine-bisphosphate. In one embodiment, themodified nucleotide contains more than one observable label, and is,e.g., 3′,5-cytidine-bisphosphate-Connecting Group-PEG_(n)-Obs.

Labeling occurs with high efficiency. In embodiments where the modifiednucleotide is detected, the method achieves comparable sensitivity toradioisotope labeling, yet avoids the use of radioactivity with itsconcomitant disadvantages.

In one embodiment, n is an integer ranging from 2 to 24 inclusive, thesugar is ribose, the purine or pyrimidine base is A, C, G, U, or I, m is3, n is 12, and the observable label is a streptavidin-binding labelselected from biotin, desthiobiotin, or iminobiotin, or a mass tag, andthe modifying molecule, if present, is a crosslinking agent.

In one embodiment, the modified nucleotide compounds have the followinggeneral structure (II):

or its salt, conjugate base, tautomer, or ionized form where

Base* is a purine or pyrimidine base;

R is H, OH, CH₃, or a hydroxyl protecting group;

Alk is a connecting group between Base* and Lnk, having the structure-//—(CH₂)_(m)—Y—//- in which Y is a bond forming group selected from

andm is an integer ranging from 3 to 6 inclusive;

Lnk is a linking group having the following structures:

in which n is an integer ranging from 2 to 48 inclusive;

A₁ is a bond forming group selected from

A₂ is a bond forming group selected from

A₃ is a bond forming group selected from

X is a cleavable group that can undergo silicon-carbon cleavage,nucleophilic cleavage, redox cleavage, acid cleavage, base cleavage,photochemical cleavage, enzymatic cleavage, or exchange-based cleavage;Z is a branching group that contains a modifying molecule (Mod); Mod isa modifying molecule (e.g., a crosslinking agent); and Obs is anobservable label moiety (e.g., an observable label in itself such as achromogen or fluor, or a molecule that can be rendered observable; adetecting agent; etc.)

The sugar is ribose or deoxyribose. The purine or pyrimidine base is C,U, A, G, T, or I and may be modified or unmodified. Embodiments include,but are not limited to, 1-methyladenine, N6-methyladenine,N6-isopentyladenine, N,N-dimethyladenine, 7-deazaadenine,2-thiocytosine, 3-methylcytosine, N4-acetylcytosine, 2-thiocytosine,1-methylguanine, 2-methylguanine, 7-methylguanine,N2,N2-dimethylguanine, 7-deazaguanine, 2-thiouracil, 6-thiopurine, or2,6-diaminopurine.

In one embodiment, the observable label is an label that is directly orindirectly observable. Examples include, but are not limited to, achromogen or fluorophore, e.g., fluorescein, rhodamine, commerciallyavailable dyes (e.g., DyLight® (Dyomics), Alexa®, Cy3, Cy5), etc., amass tag, a spin label, or a moiety capable of binding an observablelabel. In one embodiment, the observable label is a molecule capable ofbinding or being captured by a corresponding binding partner, such as astreptavidin-binding label such as biotin, desthiobiotin or iminobiotin,or an antibody. In one embodiment, the observable label is a secondarydetection label such as azide, alkyne, aldehyde, amine, hydrazide, ordiene, which is capable of forming a covalent bond with an alkyne,phosphine, azide, hydrazide, alkoxyamine, or alkene present on, e.g., anobservable label. In one embodiment, the modifying molecule is acrosslinking agent, such as a photoactivatable crosslinking agent, andis capable of covalently attaching the modified nucleotide, and anucleic acid in which the modified nucleotide has been incorporated, toanother molecule.

In one embodiment, n is an integer ranging from 2 to 24 inclusive. Inone embodiment, the sugar is ribose, the purine or pyrimidine base is A,C, G, U, or I, m is 3, n is 12, and the observable label is astreptavidin-binding label selected from biotin, desthiobiotin, oriminobiotin, or a mass tag, and the modifying molecule, if present, is acrosslinking agent.

In one embodiment, the sugar is ribose, the purine or pyrimidine base isC, m is 3, Lnk is

n is 12, A₁ is

A₂ is

when present Z is

when present, A₃ is

when present Mod is a crosslinking agent, and Obs is desthiobiotin,fluorophore, mass tag, and/or azide.

In one embodiment, the mass tag is a dimethyl piperidine- or dimethylpiperizine-(DMP)-based chemical affinity tag that may be isotopicallylabeled. The DMP-based chemical affinity tags are detection and capturebioconjugation reagents, which contain a small, non-biological epitope.The DMP-based chemical affinity tags are strong antigens for antibodiesthat are developed against the epitope. In one embodiment, a method forselectively capturing and eluting a sample containing a biomoleculelabeled with the modified nucleotide, and/or a complex containing abiomolecule labeled with the modified nucleotide, is described in U.S.Application Ser. No. 61/648,959 “Selective Elution Anti-TMT Technology”which is hereby expressly incorporated by reference herein in itsentirety, where the antibodies are immobilized, and samples containingthe DMP-based chemical affinity tag are captured with the immobilizedantibody. The labeled samples are then washed and competitively elutedwith an elution reagent that contains a displacement molecule, e.g., asmall molecule version of the epitope that is the tag itself or afragment, substructure, or structural analog of the epitope. In oneembodiment, the small molecule version of the epitope is piperidine,2-S-methyl piperidine, 2-methyl piperidine, 2,2,4,4-tetramethylpiperidine, triethylamine, and/or diisopropylethylamine. In oneembodiment, the displacement molecule is not a substructure of theepitope and epitope analogs, and instead is triethylammonia (TEA),N,N-disopropylethylammonia (DIPEA), and/or triethylammonium bicarbonate(TEAB). In one embodiment, the elution reagent contains more than onedisplacement molecule, where the displacement molecules may be acombination of a substructure of the epitope and epitope analogs, acombination of compounds that are not a substructure of the epitope andepitope analogs, and combinations of substructure of the epitope andepitope analogs and compounds that are not a substructure of the DMPepitope and epitope analogs. In one embodiment, the elution reagentcontains at least one buffer, e.g., ((hydroxymethyl)aminomethane)(Tris), 4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid (HEPES),2-[[1,3-dihydroxy-2-(hydroxymethyl)propan-2-yl]amino]ethanesulfonic acid(TES), phosphate, 2-(N-morpholino)ethanesulfonic acid (MES),3-morpholinopropane-1-sulfonic acid (MOPS),1,4-piperazinediethanesulfonic acid (PIPES), bicarbonate, carbonate,N-(2-hydroxy-1,1-bis(hydroxymethyl)ethyl)glycine (tricine),N,N-(bis(2-hydroxyethyl)glycine (bicine), etc. The elution reagent isremoved by methods know in the art, e.g., vacuum drying, desalting withdialysis or reversed phase or size exclusion chromatography. Multipleversions of the chemical tags are constructed with heavy stable isotopesor unique linkers between the epitope and reactive groups, allowinglabeling of multiple samples, mixing of these samples, and multiplexedcapture prior to mass spectrometry analysis. The competitive elutionreagent may be removed by dialysis, size-exclusion desalting resin,precipitation, or vacuum drying.

In one embodiment, the modified nucleotide is a cytidine3′-5′-bisphosphate having a PEG₁₂ linker with the structure shown below.

This structure had similar ligation efficiencies to biotinPEG₄-alkane-bisphosphate cytidine. The alkane, versus alkyne, linkagemakes the linker containing the detector less reactive, and thus lesssusceptible to degradation in cell and/or tissue lysates.

Methods using the modified nucleotide, and/or a nucleic acid labeledwith the modified nucleotide, are described. In one embodiment, themethod labels a nucleic acid with the disclosed modified nucleotide. Forexample, RNA is labeled by heating a desired RNA sample to at least 75°C. and up to 95° C.; the solution containing the RNA sample may containdimethylsulfoxide (DMSO) at a concentration ranging from 0% to 25%. TheRNA sample was heated for 1 minute to 5 minutes, then rapidly cooled onice to between 2° C. and 10° C. for at least one minute. The RNA thenwas contacted with one of the modified nucleotide compounds describedabove. The modified nucleotide was ligated to the RNA using an enzymesuch as, but not limited to, T4 RNA ligase, to result in a labeled RNA.In this embodiment, RNA was heated to at least 75° C., and up to 95° C.,then cooled for at least one minute to less than 10° C. The cooled RNAwas then contacted with the modified nucleotide under reactionconditions using T4 RNA ligase and, including in the ligation reaction,PEG having molecular weight between about 1500 and 24,000 inclusive andat a concentration ranging from 5%^(w/v) PEG to 20%^(w/v) PEG inclusive.The reaction was incubated between 30 minutes and 16 hours at atemperature ranging between 16° C. and 37° C. to ligate the modifiednucleotide to the RNA, resulting in a labeled RNA.

One embodiment is a method for labeling an RNA probe with a biotinylatednucleotide under conditions that label the RNA probe. The modifiednucleotide was incubated with an enzyme capable of ligating the modifiednucleotide to the RNA probe, e.g., a ligase such as T4 ligase, to resultin a labeled RNA probe, e.g., a desthiobiotin-labeled and/or masstag-labeled RNA probe. In one embodiment, single stranded T4 ligase wasused. In one embodiment, double stranded T4 ligase is used. In oneembodiment, thermostable T4 ligase is used. Examples of suitable ligasesinclude T4 RNA Ligase 1 (applications include labeling of 3′-termini ofRNA with 5′-[³²P] pCp, inter- and intramolecular joining of RNA and DNAmolecules; synthesis of single-stranded oligodeoxyribonucleotides; andincorporation of unnatural amino acids into proteins); T4 RNA Ligase 2(applications include ligating a nick in dsRNA, splintered RNA ligation,and ligating the 3′ OH of RNA to the 5′ phosphate of DNA in a doublestranded structure); T4 RNA Ligase 2, truncated (applications includejoining a single stranded adenylated primer to RNAs for cloning, andsmall RNA cloning); T4 RNA Ligase 2, truncated K227Q (applicationsinclude joining a single stranded adenylated primer to RNAs for cloning,small RNA cloning, and ligating with the lowest possible ligationbyproduct); each of which is commercially available from New EnglandBioLab; and thermostable RNA ligase, which is able to perform ligationsat elevated temperatures, such as above about 40° C., commerciallyavailable from Epicentre. In one embodiment, the modified nucleotide ispurified prior to ligation. Subsequent assaying for the labeled RNAprobe permits detection of the presence, quantity, etc. of theribonucleotide in the sample. The labeled RNA probe is used with, e.g.and without limitation, pull-down assays, such as for isolatingRNA-binding proteins, mobility shift assays, Northern blots, in situhybridization, etc. In embodiments, the biotin or desthiobiotin of abiotin-labeled RNA probe or desthiobiotin-labeled RNA probe is used as acapture moiety, e.g., by binding to streptavidin, or allows detectionusing a streptavidin-conjugated reporter molecule such as, e.g. andwithout limitation, enzymes (e.g., peroxidases), fluorescent dyes, etc.

For an assay using a labeled RNA to enrich for a component, whether thesubstance containing the component was bound to a chip, resin, etc.,e.g., a pull-down assay, labeled RNA was incubated in a binding reactioncontaining the protein, RNA, or DNA of interest, an optimized bindingbuffer, and affinity resin. The resin was then washed, the RNA complexwas eluted, and the protein, DNA, or RNA of interest was detected usingtechniques including but not limited to PCR, RT-PCR, Western blot, ormicroarray.

In one embodiment, the method analyzes RNA-binding proteins. Abiological sample that contains at least one RNA-binding protein wascontacted with an RNA molecule labeled with a described modifiednucleotide under conditions suitable for forming a complex between thelabeled RNA molecule and an RNA-binding protein. The biological samplemay be, e.g., a purified protein, a tissue sample, whole tissue, wholeorgan, cell culture, cell extract, cell lysate, or in vitro translatedprotein lysate. In one embodiment, the labeling nucleotide, and thus,the resultant labeled RNA molecule, contains a first binding partner,such as a biotin moiety, e.g., desthiobiotin, or a mass tag. A secondbinding partner, such as streptavidin or an antibody to the mass tag,was used to bind and capture the labeled RNA molecule/RNA-bindingprotein complex by interaction with the first binding partner, e.g.,biotin moiety or mass tag, of the modified nucleotide used to label theRNA molecule. In one embodiment, the second binding partner was attachedto a solid support, such as a bead, plate, column, etc. as known in theart. The RNA molecule/RNA-binding protein complex was attached to thesolid support by interaction between the first and second bindingpartners. The RNA molecule/RNA-binding protein complex was thencollected by removing it from the solid support, i.e., the complex iswashed off the solid support using suitable conditions and solvents,such as competitively eluting the complex with a small molecule versionof the mass tag epitope which is comprised of the tag itself or afragment, substructure, or structural analog of the epitope. Inembodiments, the eluted RNA-binding protein was detected and/orquantitated by Western blot. In embodiments, the interaction between thelabeled RNA probe and the RNA-binding protein is stabilized bycrosslinking the RNA-binding protein to the labeled RNA probe by themodifying molecule of the modified nucleotide or by adding crosslinkers(e.g., by exposure to ultraviolet (UV) light) after the RNAmolecule/RNA-binding protein complex has bound to the affinity matrix.In one embodiment, the modifying molecule is a photoactivatablecrosslinking agent.

For mobility shift assays, an excess of the labeled RNA was incubatedwith a solution containing the protein, RNA, or DNA of interest in anoptimized binding buffer. The incubation conditions were empiricallydetermined; incubation time typically ranged from 5 minutes to 1 hour,incubation temperatures typically ranged from 4° C. to room temperature(about 19° C. to about 22° C.). The binding reaction was then subjectedto electrophoresis to separate RNA binding complexes from free probe.The shifted RNA complex was then detected in-gel, or transferred to apositively charged membrane and detected using secondary detectionreagents, e.g., with a chromogen or by chemiluminescence.

For Northern blotting, the labeled RNA was used to detect RNA that hadbeen separated by electrophoresis and transferred onto a membrane. Thelabeled RNA was denatured for 5 minutes to 10 minutes at 95° C. andquickly cooled on ice to less than 10° C. The denatured probe was thenadded to an optimized hybridization solution and incubated with themembrane at an empirically determined temperature for at least 1 hour,but up to overnight. The membrane was then washed and RNA was detectedusing secondary detection reagents, e.g., with a chromogen or bychemiluminescence).

For in situ hybridization, the labeled RNA was used as a probe for thedetection of the RNA or RNA complex of interest in cells. The labeledRNA may be used after cells have been fixed onto a support (i.e., amicroscope slide, coverslip, tissue dish, microwell, etc.), or insuspension for flow cytometric analysis. Similarly, the labeled RNA maybe transfected into live cells, and detected directly or using secondaryreagents. The RNA or RNA complex was visualized using techniquesincluding but not limited to light or fluorescent microscopy, flowcytometric analysis, or microarray.

One embodiment is a method to assay RNA using an RNA probe labeled withthe compound described above and using the method described above. Thelabeled RNA can be synthesized as described above. The labeled RNA probewas contacted with the sample to be assayed under conditions to permitthe labeled RNA to hybridize with RNA in the sample. The hybridized RNAwas then detected in an assay, e.g., mobility shift, Northern blot, insitu hybridization, pull-down assay, etc. using, e.g., an observablelabel such as a biotin and a streptavidin-conjugated reporter moleculesuch as an enzyme, a fluorescent compound, an isotope, a gold particle,etc.

One embodiment is a kit containing any of the above described compoundsand instructions for labeling a nucleic acid using the compound. The kitcan also contain an enzyme, a control RNA either labeled or unlabeledwith the modified nucleotide, and a buffer.

One embodiment is a kit to label RNA with the compound described above.In one embodiment, the kit contains the compound(s), ligase, ligasebuffer, and labeling instructions. In one embodiment, the kit containsadditional kit components to enhance ligation efficiency includingpolyethylene glycol as a size exclusion reagent and DMSO to relaxsecondary structure. In one embodiment, the kit also includes a controlRNA that ligates with greater than 75% efficiency, and a syntheticbiotinylated RNA control to assess ligation efficiency. Instructionsinclude methods for a typical ligation reaction using the reagentslisted and/or instructions for using a nucleic acid comprising thelabeled nucleotide in a method, such as mobility shift, Northern blot,pull-down assay, or in situ hybridization. In one embodiment, the kitcontains a described compound where the sugar is ribose, the purine orpyrimidine base is C, m is 3, Lnk is

n is 12, A₁ is

A₂ is

when present Z is

when present A₃ is

when present Mod is a crosslinking agent, and Obs is biotin,desthiobiotin, and/or a mass tag.

One embodiment is a kit for isolating RNA-binding proteins. The kitcontains the disclosed modified nucleotide, where Obs is biotin,desthiobiotin, and/or a mass tag and instructions for using RNA labeledwith the compound as bait to isolate an RNA-binding protein in apull-down assay. In one embodiment, the kit further contains reagentsfor crosslinking.

Synthesis of exemplary specific compounds among each of the followingmodified nucleotides is subsequently described. One skilled in the artwill appreciate that such synthesis schemes are representative and notlimiting; one skilled in the art knows or can readily determine how tosynthesize other specific examples using known methods and without undueexperimentation. Other such examples include, but are not limited to,biotin-PEG₄ modifications,biotin-PEG₄-alkane-3′,5′-cytidine-bisphosphate (BPA-3′,5′-pCp, compound6), overview of biotin-PEG₄-SS-alkane-3′,5′-cytidine-bisphosphate(BP₄SSA-3′,5′-pCp, compound 12), biotin-PEG₄-SS-alkane-cytidine(BP₄SSAC, compound 11), and detailed reactions forbiotin-PEG₄-SS-alkane-3′,5′-cytidine-bisphosphate (BP₄SSA-3′,5′-pCp,compound 12); biotin-PEG₁₂ modifications; azido-PEG₄ modifications;fluorophore-PEG₄ modifications, DyLight550-PEG₄-alkane-3′,5′-cytidine-bisphosphate (Dy550P₄A-3′,5′-pCp,compound 14).

Biotin-PEG₄ Modification

To prepare biotin-polyethylene glycol(PEG)-alkane-3′,5′-cytidine-bisphosphate, propargyl amine was reactedwith methyl trifluoroacetate to result in propargyltrifluoroacetamide.The propargyltrifluoroacetamide reacts with 5-iodocytidine to result in5-[3-(trifluoroacetamido)propynyl]cytidine. The5-[3-(trifluoroacetamido)propynyl]cytidine is converted to5-[3-(trifluoroacetamido)propyl]cytidine. The5-[3-(trifluoroacetamido)propyl]cytidine then is converted to5-(3-aminopropyl)cytidine. The 5-(3-aminopropyl)cytidine then is reactedwith NHS-PEG-biotin to result in biotin-PEG-alkane-cytidine. Thebiotin-PEG-alkane-cytidine then is reacted with diphosphoryl chloride toresult in biotin-polyethylene glycol(PEG)-alkane-3′,5′-cytidine-bisphosphate.

Proparglytrifluoroacetamide (1) was prepared according to the followingreaction:

Propargyl amine (4.00 g, 72.62 mmol, 1.00 equiv.) was added dropwise tomethyl trifluoroacetate (11.16 g, 87.15 mmol, 1.20 equiv.) at 0° C. Thereaction mixture was stirred at 0° C. for 2 h and then concentratedunder reduced pressure to remove methanol. The product was purified byvacuum distillation yielding propargyltrifluoroacetamide as a colorlessliquid (9.59 g, 87%). The structure was confirmed by ¹H- and ¹⁹F-NMR.

5-[3-(trifluoroacetamido)propynyl]cytidine (2) was prepared according tothe following reaction:

A 100-mL three-necked flask was charged with 5-iodocytidine (2.66 g,7.00 mmol, 1.00 equiv.), cuprous iodide (0.267 g, 1.40 mmol, 0.20equiv.) and dry DMF (35 mL). After complete dissolution of the reactionmixture, propargyltrifluoroacetamide (3.17 g, 21.00 mmol, 3.00 equiv.),triethylamine (1.42 g, 14.00 mmol, 2.00 equiv.) and finally tetrakis(triphenylphosphine)palladium(0) (0.809 g, 0.70 mmol, 0.10 equiv.) wereadded to the reaction mixture under N₂. The reaction was stirred atambient temperature (around 19° C. to around 22° C.) under N₂ for 18-24h. The reaction was then diluted with 70 mL of 1:1methanol-dichloromethane and the bicarbonate form of AGI X8 resin (12.00g) was added. After stirring for about one h, the reaction mixture wasfiltered and the resin was washed with 1:1 methanol-dichloromethane. Thecombined filtrates were rapidly concentrated with a rotary evaporator.The residue was immediately purified by flash chromatography. Removal ofsolvent from the appropriate fractions afforded 1.84 g (67%) of5-[3-(trifluoroacetamido)propynyl]cytidine as a light brown solid, whichwas confirmed by ¹H-NMR.

5-[3-(trifluoroacetamido)propyl]cytidine (3) was prepared according tothe following reaction:

5-[3-(trifluoroacetamido)propynyl]cytidine (1.25 g, 3.19 mmol, 1.00equiv.) was dissolved in methanol (30 mL). Palladium hydroxide (0.25 g,20 wt./wt. % based on propynyl cytidine) and triethylsilane (3.71 g,31.90 mmol, 10.00 equiv.) were added to the reaction mixture. After20-24 hours at ambient temperature, the reaction mixture was filteredthrough glass fiber and the filtrate was concentrated under reducedpressure giving a dark brown residue. The residue was purified by flashchromatography. Removal of solvent from the appropriate fractionsafforded 0.85 g (71%) of 5-[3-(trifluoroacetamido)propyl]cytidine as acream colored solid, which was confirmed by ¹H-NM.

5-(3-aminopropyl)cytidine (4) was prepared according to the followingreaction:

5-[3-(trifluoroacetamido)propyl]cytidine (0.69 g, 1.74 mmol) wasdissolved in DI H₂O (8.5 mL). After complete dissolution, concentratedammonium hydroxide (NH₄OH) (8.5 mL) was added to the reaction mixture.The reaction solution was stirred at ambient temperature for 2-3 h andthen concentrated under reduced pressure giving the crude product asyellow-orange residue. The crude product was dissolved in deionized H₂O(10 mL) and AG50W-X8 resin (2.5 g) was added to the solution. Thesuspension was stirred for 15 min and filtered over a bed of AG50W-X8resin (2.5 g). The resin was washed with DI H₂O and the product was theneluted off of the resin by washing the resin with deionized H₂O/conc.NH₄OH, 4:1, collecting fractions (monitored by TLC). Removal of solventfrom the appropriate fractions afforded 0.51 g (98%) of5-(3-aminopropyl)cytidine as light tan solid, which was confirmed by¹H-NMR.

Biotin-PEG₄-alkane-cytidine (BPAC, 5) was prepared according to thefollowing reaction:

NHS-PEG₄-biotin (0.196 g, 0.333 mmol, 1.00 equiv.) was dissolved in DMF(10 mL). 5-(3-aminopropyl)cytidine) (0.100 g, 0.333 mmol, 1.00 equiv.)was added to the reaction solution. The reaction solution was stirred atambient temperature under N₂ atmosphere. After 20-24 h, the reactionmixture was concentrated under reduced pressure giving the crudeproduct. The crude product was purified by flash chromatography. Removalof solvent from the appropriate fractions afforded 0.18 g (69%) of BPACas a white solid, which was confirmed by ¹H-NMR.

Biotin-PEG₄-alkane-3′,5′-cytidine-bisphosphate (BPA-3′,5′-pCp, 6) wasprepared according to the following reaction:

BPAC (0.061 g, 0.079 mmol, 1.00 equiv.) was partially dissolved indiphosphoryl chloride (196 μL, 1.66 mmol, 21.00 equiv.), previouslycooled to −10° C. to −15° C. in a 1-mL Reacti-Vial™. The mixture wasthen stirred at −10° C. to −15° C. After 5 h, the reaction was quenchedby addition of ice cold water (1-2 mL) and, immediately thereafter, witha chilled solution of 0.5 M TEAB buffer, pH 8.5 (17 mL). Uponstabilization at neutral pH, the colorless solution was stirred atambient temperature for 30 min and concentrated using a rotaryevaporator until complete removal of TEAB. The solution was desaltedusing a C18 cartridge (Waters) and purified by FPLC (MonoQ 10/100GLcolumn, GE) using a pH gradient. After a final desalting using again aC18 cartridge (Waters), BPA-3′,5′-pCp was isolated after lyophilizationas a white solid (10 mg, 9%), which was confirmed by ¹H-NMR & HPLC.

Overview of Preparation ofBiotin-PEG₄-SS-alkane-3′,5′-cytidine-bisphosphate (BP₄SSA-3′,5′-pCp,Compound 12)

The reaction scheme to prepare biotin-polyethylene glycol(PEG)-SS-alkane-3′,5′-cytidine-bisphosphate is as follows. The5-(3-aminopropyl)cytidine (compound 4) is reacted with NHS-SS-PEG-biotinto result in biotin-PEG-SS-alkane-cytidine (compound 11). Thebiotin-PEG-SS-alkane-cytidine (compound 11) then is reacted withdiphosphoryl chloride to result in biotin-polyethylene glycol(PEG)-SS-alkane-3′,5′-cytidine-bisphosphate (compound 12).

Preparation of Biotin-PEG₄-SS-alkane-cytidine (BP₄SSAC, Compound 11)

NHS-SS-PEG₄-biotin (0.250 g, 0.333 mmol, 1.00 equiv.) was dissolved inDMF (10 mL). 5-(3-aminopropyl)cytidine) (0.100 g, 0.333 mmol, 1.00equiv.) was added to the reaction solution. The reaction solution wasstirred at ambient temperature under N₂ atmosphere. After 20-24 hours,the reaction mixture was concentrated under reduced pressure giving thecrude product. The crude product was purified by flash chromatography.Removal of solvent from the appropriate fractions afforded 0.19 g (61%)of BP₄SSAC (compound 11) as a white solid, which was confirmed by¹H-NMR.

Preparation of Biotin-PEG₄-SS-alkane-3′,5′-cytidine-bisphosphate(BP₄SSA-3′,5′-pCp, Compound 12)

BP₄SSAC (0.074 g, 0.079 mmol, 1.00 equiv.) was partially dissolved indiphosphoryl chloride (196 μL, 1.66 mmol, 21.00 equiv.), previouslycooled to −10° C. to −15° C. in a 1-mL Reacti-Vial™. The mixture wasthen stirred at −10° C. to −15° C. After five hours, the reaction wasquenched by addition of ice cold water (1-2 mL) and, immediatelythereafter, with a chilled solution of 0.5M TEAB buffer, pH 8.5 (17 mL).Upon stabilization at neutral pH, the colorless solution was stirred atambient temperature for 30 min and concentrated using a rotaryevaporator until complete removal of TEAB. The solution was desaltedusing a C18 cartridge (Waters) and purified by FPLC (MonoQ 10/100GLcolumn, GE) using a pH gradient. After a final desalting using again aC18 cartridge (Waters), BP₄SSA-3′,5′-pCp (compound 12) was isolatedafter lyophilization as a white solid (5 mg, 6%), which was confirmed by¹H-NMR and HPLC.

Biotin-PEG₁₂ Modification Preparation of Biotin-PEG₁₂-alkane-cytidine(BP₁₂AC, Compound 7)

NHS-PEG₁₂-biotin (0.313 g, 0.333 mmol, 1.00 equiv.) was dissolved in DMF(10 mL). 5-(3-aminopropyl)cytidine) (0.100 g, 0.333 mmol, 1.00 equiv.,compound 4) was added to the reaction solution. The reaction solutionwas stirred at ambient temperature under N₂ atmosphere. After 20-24 h,the reaction mixture was concentrated under reduced pressure giving thecrude product. The crude product was purified by flash chromatography.Removal of solvent from the appropriate fractions afforded 0.27 g (72%)of BP₁₂AC (compound 7) as a light yellow foam, which was confirmed by¹H-NMR.

Preparation of Biotin-PEG₁₂-alkane-3′,5′-bisphosphate-cytidine(BP₁₂A-3′,5′-pCp, Compound 8)

Biotin-PEG₁₂-alkane-cytidine (0.135 g, 0.120 mmol, 1.00 equiv., compound7) was partially dissolved in diphosphoryl chloride (315 μL, 2.40 mmol,20.00 equiv.), previously cooled to −10 to −15° C. in a 1-mLReacti-Vial™. The mixture was stirred at −10 to −15° C. After fivehours, the reaction was quenched by adding ice cold water (1-2 mL) andimmediately after with a chilled solution of 0.5M TEAB buffer, pH 8.5(40 mL). Upon stabilization at neutral pH, the colorless solution wasstirred at ambient temperature for 30 min and concentrated using arotary evaporator until TEAB was completely removed. The solution wasdesalted using a C18 cartridge (Waters) and purified by FPLC (MonoQ10/100GL column, GE) using a pH gradient. After final desalting using aC18 cartridge (Waters), biotin-PEG₁₂-alkane-3′,5′-cytidine-bisphosphate(compound 8) was isolated after lyophilization as a sticky white solid(8 mg, 5%), which was confirmed by 1H-NMR and HPLC.

Azido-PEG₄ Modification Azido-PEG₄-alkane-3′,5′-cytidine-bisphosphate,Compound 9

One embodiment is a method of preparingazido-PEG₄-alkane-3′,5′-cytidine-bisphosphate. The5-(3-aminopropyl)cytidine was synthesized as described above, then wasreacted with NHS-PEG₄-azide to result in azido-PEG₄-alkane-cytidine. Theazido-PEG₄-alkane-cytidine was then reacted with diphosphoryl chlorideto result in azido-PEG₄-alkane-3′,5′-cytidine-bisphosphate.

NHS-PEG₄-azide (0.408 g, 1.05 mmol, 1.00 equiv.) was dissolved in DMF(32 mL). The 5-(3-aminopropyl)cytidine) (0.315 g, 1.05 mmol, 1.00equiv.) was added to the reaction solution. The reaction solution wasstirred at ambient temperature under N₂ atmosphere. After 20-24 hours,the reaction mixture was concentrated under reduced pressure giving thecrude product. The crude product was purified by flash chromatography.Removal of solvent from the appropriate fractions afforded 0.378 g (63%)of azido-PEG₄-alkane-cytidine (compound 9) as a near colorless glass,which was confirmed by 1H-NMR.

Azido-PEG₄-alkane-3′,5′-Bisphosphate-Cytidine (AzP₄A-3′,5′p-C-p),Compound 10

Azido-PEG₄-alkane-cytidine (0.150 g, 0.262 mmol, 1.00 equiv., compound9) was partially dissolved in diphosphoryl chloride (688 μL, 5.24 mmol,20.00 equiv.), previously cooled to −10 to −15° C. in a 1 mLReacti-Vial™. The mixture was then stirred at −10 to −15° C. After fivehours, the reaction was quenched by adding ice cold water (2-3 mL) andthen immediately with a chilled solution of 0.5M TEAB buffer, pH 8.5 (87mL). Upon stabilization at neutral pH, the colorless solution wasstirred at ambient temperature for 30 min and concentrated using arotary evaporator until TEAB was complete removed. The solution wasdesalted using a C18 cartridge (Waters) and purified by FPLC (MonoQ10/100GL column, GE) using a pH gradient. After final desalting usingagain a C18 cartridge (Waters),azido-PEG₄-alkane-3′,5′-cytidine-bisphosphate (compound 10) was isolatedafter lyophilization as a sticky white solid (10 mg, 6%), confirmed by1H-NMR and HPLC.

Fluorophore-PEG₄ Modifications Preparation of DyLight550-PEG₄-alkane-3′,5′-cytidine-bisphosphate (Dy550P₄A-3′,5′-pCp, 14)

DyLight 550-polyethylene glycol (PEG)-alkane-3′,5′-cytidine-bisphosphate(compound 14) is prepared as follows. Theazido-PEG₄-alkane-3′,5′-cytidine-bisphosphate (compound 10) wassynthesized as described above, then allowed to react withtris(2-carboxyethyl)phosphine hydrochloride (TCEP) to result inamino-PEG₄-alkane-3,′5′-cytidine bisphosphate (compound 13). Theamino-PEG₄-alkane-3,′5′-cytidine bisphosphate (compound 13) was thenreacted with DyLight 550 NHS ester to result in 550-polyethylene glycol(PEG)-alkane-3′,5′-cytidine-bisphosphate (compound 14).

Preparation of Amino-PEG₄-alkane-3′,5′-bisphosphate-cytidine(AmP₄A-3′,5′-pCp, 13)

Azido-PEG₄-alkane-3′,5′-bisphosphate-cytidine (3.56 pmol, 1.00 equiv.,compound 10) was dissolved in 200 mM Tris/HCl, pH 7.5 (800 μL).Tris(2-carboxyethyl)phosphine hydrochloride (TCEP) (17.54 mg, approx.5.00 equiv.) was dissolved in 200 mM Tris/HCl, pH 7.5 (688 μL). The TCEPsolution (200 μL) was added to the solution of azide and the reactionwas mixed at ambient temperature. After 1-3 h, the reaction mixture waspurified by FPLC and the fractions containing product were treateddirectly with DyLight 550 NHS ester to result inamino-PEG₄-alkane-3′,5′-bisphosphate cytidine (compound 13).

Preparation of DyLight 550-PEG₄-alkane-3′,5′-bisphosphate-cytidine(Dy550P₄A-3′,5′-pCp, 14)

The pH of an FPLC fraction (2 mL) containingamino-PEG₄-alkane-3′,5′-bisphosphate-cytidine (compound 13) was adjustedto pH 7.0 by adding 1M HEPES, pH 7.3. Separately, a 1 mM solution ofDyLight 550 NHS ester was prepared by dissolving DyLight 550 NHS ester(MW=1040.05, 1 mg) in ultra pure water (960 μL).Amino-PEG₄-alkane-3′,5′-bisphosphate-cytidine (0.25 mL) and DyLight 550NHS ester (0.25 mL) were combined in a separate reaction vessel and weremixed with rotation for 1 h at ambient temperature. The reaction mixturewas purified by FPLC (MonoQ 10/100GL column, GE) using a pH and saltgradient. Fractions containing product were dialyzed and subsequentlylyophilized, yielding DyLight550-PEG₄-alkane-3′,5′-cytidine-bisphosphate(compound 14) as a dark pink residue.

Desthiobiotin-PEG_(n) Modifications Overview Preparation ofDesthiobiotin-PEG₄-alkane-3′,5′-cytidine-bisphosphate (DP₄A-3′,5′-pCp,Compound 17)

The reaction scheme to prepare desthiobiotin-polyethylene glycol(PEG)₄-alkane-3′,5′-cytidine-bisphosphate was as follows. Theazido-PEG₄-alkane-cytidine (compound 9) was reduced using triethylsilaneand 20 wt % palladium hydroxide giving amino-PEG₄-alkane-cytidine(compound 15). The amino-PEG₄-alkane-cytidine (compound 15) was thenreacted with NHS-desthiobiotin giving desthiobiotin-PEG₄-alkane-cytidine(compound 16). Desthiobiotin-PEG₄-alkane-cytidine was then reacted withdiphosphoryl chloride givingdesthiobiotin-PEG₄-alkane-cytidine-bisphosphate (compound 17).

Preparation of Amino-PEG₄-alkane-cytidine (AmP₄AC, 15)

Azido-PEG₄-alkane-cytidine (9) (0.20 g, 0.349 mmol, 1.00 equiv.) wasdissolved in methanol (6 mL). Palladium hydroxide (0.040 g, 20 wt./wt. %based on 9) and triethylsilane (0.406 g, 3.49 mmol, 10.00 equiv.) wasadded to the reaction mixture. After 20-24 hours at ambient temperature,the reaction mixture was filtered through a pad of glass fiber and thefiltrate was concentrated under reduced pressure givingamino-PEG₄-alkane-cytidine (15) as an off-white residue (0.19 g, 99%)which was confirmed by ¹H-NMR and used directly without furtherpurification.

Preparation of Desthiobiotin-PEG₄-alkane-cytidine (DP₄AC, 16)

NHS-desthiobiotin (0.102 g, 0.329 mmol, 1.00 equiv.) was added to asolution of amino-PEG₄-alkane-cytidine (15) (0.18 g, 0.329 mmol, 1.00equiv.) in DMF (3 mL). The reaction solution was stirred at ambienttemperature under N₂ atmosphere. After 20-24 h, the reaction mixture wasconcentrated under reduced pressure giving the crude product as a paleyellow residue. The crude product was purified by flash chromatography.Removal of solvent from the appropriate fractions gavedesthiobiotin-PEG₄-alkane-cytidine (16) as a clear, near colorless glass(0.185 g, 76%) which was confirmed by ¹H-NMR.

Preparation of Desthiobiotin-PEG₄-alkane-3′,5′-cytidine-bisphosphate(BP₄A-3′,5′-pCp, 17)

Desthiobiotin-PEG₄-alkane-cytidine (16) (0.117 g, 0.157 mmol, 1.00equiv.) was partially dissolved in diphosphoryl chloride (391 μL, 3.30mmol, 21.00 equiv.) in a 3 mL Reacti-Vial™. The mixture was then stirredat 0 to −10° C. After five hours, the reaction was quenched by theaddition of ice cold ultra-pure water (1 mL) immediately followed by asolution of 0.5M TEAB buffer, pH 8.5 (23 mL). The colorless solution wasstirred at ambient temperature for 30 min and then stored overnight at0-5° C. The pH was adjusted to 3.0-3.5 and the solution was concentratedusing a rotary evaporator until TEAB was complete removed. The solutionwas desalted using a C18 cartridge (Waters) and purified by FPLC (MonoQ10/100GL column, GE). The purified product was subsequently desaltedusing a C18 cartridge (Waters) givingdesthiobiotin-PEG₄-alkane-3′,5′-cytidine-bisphosphate (17) as a clearglass (9 mg, 6%) after lyophilization. The structure was confirmed by¹H-NMR and HPLC.

Overview Preparation ofDesthiobiotin-PEG₁₂-alkane-3′,5′-cytidine-bisphosphate (DP₁₂A-3′,5′-pCp,Compound 21)

The reaction scheme to prepare desthiobiotin-polyethylene glycol(PEG)₁₂-alkane-3′,5′-cytidine-bisphosphate was as follows. The5-(3-aminopropyl)cytidine (compound 4) was synthesized as describedabove, then was reacted with NHS-PEG₁₂-azide givingazido-PEG₁₂-alkane-cytidine (compound 18). Theazido-PEG₁₂-alkane-cytidine (compound 18) was reduced usingtriethylsilane and 20 wt. % palladium hydroxide givingamino-PEG₁₂-alkane-cytidine (compound 19). Theamino-PEG₁₂-alkane-cytidine (compound 19) was then reacted withNHS-desthiobiotin giving desthiobiotin-PEG₁₂-alkane-cytidine (compound20). Desthiobiotin-PEG₄-alkane-cytidine was then reacted withdiphosphoryl chloride givingdesthiobiotin-PEG₁₂-alkane-cytidine-bisphosphate (compound 21).

Preparation of Azido-PEG₁₂-alkane-cytidine (AzP₄AC, 18)

NHS-PEG₁₂-azide (0.445 g, 0.607 mmol, 1.00 equiv.) was dissolved in DMF(10 mL). 5-(3-aminopropyl)cytidine (4) (0.182 g, 0.607 mmol, 1.00equiv.) was added to the reaction solution as a solid. The reactionsolution was stirred at ambient temperature under N₂ atmosphere. After18-24 hours, the reaction mixture was concentrated under reducedpressure giving the crude product as a pale amber oil. The crude productwas purified by flash chromatography. Removal of solvent from theappropriate fractions gave of azido-PEG₁₂-alkane-cytidine (18) as aclear, near colorless residue (0.35 g, 62%) the structure of which wasconfirmed by ¹H-NMR.

Preparation of Amino-PEG₁₂-alkane-cytidine (AmP₄AC, 19)

Azido-PEG₁₂-alkane-cytidine (18) (0.10 g, 0.108 mmol, 1.00 equiv.) wasdissolved in methanol (3 mL). Palladium hydroxide (0.020 g, 20 wt./wt. %based on 18) and triethylsilane (0.126 g, 1.08 mmol, 10.00 equiv.) wasadded to the reaction mixture. After 20-24 hours at ambient temperature,the reaction mixture was filtered through a pad of glass fiber and thefiltrate was concentrated under reduced pressure givingamino-PEG₁₂-alkane-cytidine (19) as an clear, colorless residue (0.10 g,100%) which was confirmed by ¹H-NMR and used directly without furtherpurification.

Preparation of Desthiobiotin-PEG₁₂-alkane-cytidine (DP₁₂AC, 20)

NHS-desthiobiotin (0.035 g, 0.111 mmol, 1.00 equiv.) was added to asolution of amino-PEG₁₂-alkane-cytidine (19) (0.10 g, 0.111 mmol, 1.00equiv.) in DMF (2 mL). The reaction solution was stirred at ambienttemperature under N₂ atmosphere. After 20-24 h, the reaction mixture wasconcentrated under reduced pressure giving the crude product as a paleyellow residue. The crude product was purified by flash chromatography.Removal of solvent from the appropriate fractions gavedesthiobiotin-PEG₁₂-alkane-cytidine (20) as a clear, near light yellowglass (0.054 g, 44%) which was confirmed by ¹H-NMR and used directlywithout further purification.

Preparation of Desthiobiotin-PEG₁₂-alkane-3′,5′-cytidine-bisphosphate(DP₁₂A-3′,5′-pCp, 21)

Desthiobiotin-PEG₁₂-alkane-cytidine (20) (0.054 g, 0.049 mmol, 1.00equiv.) was partially dissolved in diphosphoryl chloride (122 μL, 1.03mmol, 21.00 equiv.) in a 3 mL Reacti-Vial™. The mixture was then stirredat 0° C. to 10° C. After about five hours, the reaction was quenched byadding ice cold ultra-pure water (1 mL) immediately followed by asolution of 0.5M TEAB buffer, pH 8.5 (11 mL). The colorless solution wasstirred at ambient temperature for 30 min and then stored overnight at0-5° C. The pH was adjusted to 3.0-3.5 and the solution was concentratedusing a rotary evaporator until TEAB was completely removed. Thesolution was desalted using a C18 cartridge (Waters) and purified byFPLC (MonoQ 10/100GL column, GE). The purified product was subsequentlydesalted using a C18 cartridge (Waters) givingdesthiobiotin-PEG₁₂-alkane-3′,5′-cytidine-bisphosphate (21) as a clearglass (4 mg, 6%) after lyophilization. The structure was confirmed by¹H-NMR and HPLC.

-   -   Other exemplary compounds follow. Examples of fluorescent        compounds include, but are not limited to, the following:

Examples of compounds with mass labels include, but are not limited to,the following:

Examples of compounds with a spin label include, but are not limited to,the following:

Examples of a desthiobiotin-containing compound include, but are notlimited to, the following

Examples of compounds with alternative cleavage include, but are notlimited to, the following:

Examples of compounds with photo-reactive group include, but are notlimited to, the following:

The following examples are intended to illustrate the utility of thepresent invention but do not limit the claim scope:

EXAMPLE 1

In the experiments subsequently described, T4 RNA ligase was used tolabel RNA with biotinylated cytidine 3′,5′ bisphosphate. Severalmolecules were synthesized to optimize the nucleotide for optimalligation efficiency and functionality, for example, preservation of theinteraction of the labeled RNA with other RNA or cellular proteins.Three different alkyl linkages were tested, including alkyne, alkene,and alkane, in combination with both LC (long chain), SC (short chain),and PEG spacers, as shown in FIGS. 1-3. The molecules were tested forligation efficiency and functionality utilizing establishedelectrophoretic mobility shift (EMSA) controls. In a mobility shiftassay, labeled RNA probe is incubated with a cell lysate containing theprotein(s) of interest in a binding reaction. The reaction is thenelectrophoresed on a non-denaturing gel. Unbound probe will migrate tothe bottom of the gel, while protein bound probe will migrate moreslowly, resulting in a bandshift. The alkyne-LC- andalkyne-SC-containing nucleotides ligated with good efficiency; however,the alkyne linkage was reactive in cell lysates. In a purified systemusing an RNA polymerase template and purified RNA polymerase, the alkynecompounds produced a functional gel shift (FIG. 4 A), while the alkynecompound did not produce a functional gel shift with the iron responsiveelement (IRE)-iron responsive protein (IRP) control utilizing cytosolicliver extract (FIG. 4B). When the liver extract was mixed with purifiedRNA polymerase, the bandshift was affected, suggesting that the alkynecompound is reactive with liver extract (FIG. 4C). Similar results wereobtained with the alkene compounds, where the IRE-IRP control ligated,but did not produce a functional bandshift (FIG. 5). The nucleotidecontaining the alkane linkage and PEG spacer was the most optimalcompound for both ligation efficiency and functionality (FIG. 6).

Utilizing the biotin-PEG4-alkane 3,5 cytidine bisphosphate molecule,optimal ligation conditions were determined. The conditions describedresulted in ligation efficiencies greater than 70%, and in some casesgreater than 90%, depending upon the RNA secondary structure andligation conditions. A standard reaction had a donor to acceptorligation ratio of greater than 20:1. The reaction buffer contained 20 Uto 40 U T4 RNA ligase, 40 U RNase inhibitor, 50 mM Tris-HCl, 10 mMMgCl₂, 10 mM DTT, 1 mM ATP (pH 7.8 at 25° C.), and 15% polyethyleneglycol (PEG, MW 20,000). To achieve ligation efficiencies greater than70%, reactions were incubated at 37° C. for 30 minutes, or at 16° C.from 30 minutes to 24 hours, depending upon the RNA length and secondarystructure. In one embodiment, reactions contained 25 pmol to 50 pmolRNA, 1 nmol biotinylated nucleotide, and 20 U to 40 units of T4 RNAligase in a 30 μl reaction volume. An excess of biotinylated nucleotidedid not affect ligation efficiencies, and a range 1 pmol RNA to 200 pmolof RNA was tested in the ligation reaction. The concentration of PEGranged from 5% to 20%.

As shown in the table below, the ligation conditions were assessedutilizing several RNA species, ranging in length, complexity, andfunction to demonstrate efficiency of ligation reaction using RNA ofvarying complexity and length. RNA was derived from the 3′ untranslatedregions (UTR) of mRNA 28-42 nucleotides, miRNA (22-80 nucleotides), andcatalytic RNA (451 nucleotides). RNA was derived synthetically, or fromin vitro transcription reactions.

Length Optimal reaction Description RNA source (bases) conditions IRE(iron 5′ or 3′ UTR synthetic 28 2 hrs 16 C. responsive element element)RNA RNA synthetic 42 30 minutes, 37° C. polymerase >1 hr 16° C. templateRNA mir-16-1 mature micro synthetic 22 ON 16° C. RNA TNF ARE 3′ UTRsynthetic 37 2 hrs 16° C. element Let-7 pre-miRNA in vitro ~70 overnight16° C. transcribed hTR catalytic in vitro 451 overnight 16° C. RNAtranscribed COX-76 3′ UTR in vitro ~70 overnight 16° C. ARE elementtranscribed mir-16-1 pre-miRNA in vitro ~70 overnight 16° C. transcribed

Ligation efficiencies were greater than 70% with reactions using 25-50pmol RNA, 1 nmol biotinylated nucleotide, 20-40 U T4 RNA ligase, 40 URNase Inhibitor, 50 mM Tris-HCl, 10 mM MgCl₂, 10 mM DTT, 1 mM ATP (pH7.8 at 25° C.), and 15% PEG (MW 20,000). Ligation efficiencies wereimproved for RNAs with extensive RNA secondary structure or length byheating briefly before the ligation reaction; heating temperaturesranged from 80° C.-90° C. for 1-5 minutes, followed by rapid-cooling onice for at least 1 minute to several hours. In some cases, adding 25%DMSO before heating enhanced ligation efficiency. The order of additionof the reaction components did not matter, except for the PEG, which wasadded last. Several PEG varieties were tested including molecularweights of 1500, 6000, 8500, and 20,000. Although the PEG (MW 20,000)best enhanced ligation efficiency, the other PEG molecules wereacceptable, and other size exclusion molecules would also be acceptable.A PEG concentration of 15% was optimal. Other PEG concentrations couldalso be used, ranging from 5% to 20%.

Ligation efficiencies were assessed using dot blot and quantitative spotdensitometry. A synthetically biotinylated RNA was used as a controlwhere 100% biotinylation was assumed. Labeled RNA from the ligationreaction and the synthetically labeled RNA were first normalized toconcentration, and then serially diluted to determine efficiency. Asmall volume was applied (spotted) onto a positively charged nylonmembrane. The membrane was cross-linked using ultraviolet (UV)radiation. Biotinylated RNA was detected using a streptavidinhorseradish peroxidase (HRP) substrate and chemiluminescent detection.The non-saturating spots, which are spots where the densitometryintensity value was not saturated, were quantitated using densitometry.To determine ligation efficiency, labeled RNA was compared to thecontrol standard to determine efficiency. To determine labelingreproducibility, samples were applied (spotted) in triplicate for two ofthe RNA samples for intra-assay variability, and each ligation with theoptimized conditions was repeated at least three independent times forinterassay variability. To determine labeling integrity, labeled RNA wasseparated by electrophoresis on a gel containing 5% acrylamide/8 M urea(denaturing gel), the RNA was transferred to a nylon membrane and wasdetected using chemiluminescence. The results indicated that the labeledprobes were of high quality, of the correct size, and exhibited eitherminimal degradation or no degradation.

In vitro transcribed RNA was derived through transcription from adigested plasmid containing the sequence of interest flanked by a T7polymerase binding site and restriction enzyme site such that only theRNA of interest is transcribed. In vitro transcribed RNA was alsoderived through transcription of complementary primers containing a T7RNA polymerase binding sequence element. Digested plasmid was purifiedby extraction with phenol:chloroform and ethanol precipitation.Complementary primers were annealed in a reaction containing 25 μM ofeach primer in 10 mM HEPES buffer (pH 7.3). Reactions were incubated at95° C. for ten minutes followed by slow cooling at room temperature forat least ten minutes, followed by incubation on ice. Transcriptionreactions typically contained 500 ng-1 μg DNA, 0.5 mM each of ATP, CTP,UTP, and GTP, 1× transcription buffer, 30 U T7 RNA polymerase, and 40units RNAse inhibitor. Reactions were incubated for 30 minutes to 1 hourat 37° C. DNA was digested for ten minutes with RNAse-free DNAse I at37° C., followed by inactivation with EDTA. RNA was then selectivelyprecipitated with ethanol, and transcript purity was determined byeither agarose or non-denaturing polyacrylamide gel electrophoresis.Precipitated RNA was then quantitated by UV-spectroscopy (absorbance at260 nm/280 nm), and 25 pmol-50 pmol of RNA was used in each ligationreaction.

EXAMPLE 2

The functionality of the labeled RNA was determined by assaying a knowninteraction of the RNA to ensure that the 3′-end label minimallydisturbed secondary structure. Functionality of labeled iron responsiveelement (IRE), RNA polymerase template, and let-7 micro RNA wasdetermined by RNA electrophoretic mobility shift assay (EMSA). Theprotein sources included cytosolic liver extract containing ironresponsive element-iron responsive protein (IRE-IRP), lin-28overexpression lysate (let-7-lin28), and purified RNA core polymerase(Epicentre). Dilutions of each RNA (nM) were incubated with the proteinof interest in a 1× binding reaction containing 10 mM HEPES (pH 7.3), 20mM KCl, 1 mM MgCl₂, 1 mM DTT, 2.5-10 μg tRNA, and 5% glycerol for 15-30minutes at room temperature (about 20° C. to about 22° C.). Optimalbinding conditions were achieved for RNA polymerase template bysubstituting tRNA with bovine serum albumin (BSA), and increasing theDTT concentration to 3 mM and the KCl concentration to 40 mM for thelet-7-lin28 interaction. Binding reactions composition were separated byelectrophoresis on native 6% acrylamide DNA retardation gels for one hr,100 V, at either room temperature or 4° C. The RNA was then transferredto a positively charged nylon membrane, cross-linked (UV irradiation),and then detected using chemiluminescence. Three binding reactions wereassessed for each labeled RNA: 1) migration and intensity of the freeprobe that migrated toward the bottom of the gel; 2) intensity of thelabeled RNA with protein, resulting in a bandshift of the RNA-proteincomplex; and 3) the competition reaction of the labeled RNA and theunlabeled RNA with protein (FIG. 6). Each bandshift reaction wasrepeated three times with three independently labeled RNAs. Each of the3 end-labeled probes was able to functionally bind its respectiveproteins and produce a robust bandshift, as shown for RNA template-RNApolymerase interaction (FIG. 6A), IRE-IRP interaction (FIG. 6B), andlet-7-lin28 interaction (FIG. 6C). Each probe was also functional at thenanomolar level, indicating that the 50 pmol labeling reaction wassufficient for EMSA studies.

EXAMPLE 3

In one embodiment, biotin, a mass tag, or other suitable moietycontaining an alkane linkage and PEG₄ spacer, known by one skilled inthe art, on the labeled nucleotide serves as an affinity handle forisolating RNA:protein complexes. The functionality of a describedbiotin-labeled RNA to serve as an affinity handle for isolating RNAcomplexes (containing RNA, DNA, RNA and DNA, or protein) using anaffinity resin, bead, or sensor chip (e.g., pull-down) was determinedusing streptavidin agarose resin and surface plasmon resonance.

IRE-RNA (SEQ ID NO: 1) was labeled using biotinPEG₄-alkane-3′5′-bisphosphate cytidine, and T4 RNA ligase. The IRPprotein, which binds IRE RNA sequences, was cloned into a vectorcontaining an HA tag and in vitro translated using an human cell-freehuman in vitro transcription/translation system. Before incubation withthe biotinylated RNA, the IRP lysate was incubated with streptavidinagarose resin to reduce non-specific binding, and to remove endogenousbiotin. The IRP lysate was then incubated with the labeled IRE, or witha non-specific control RNA (SEQ ID NO: 2) which was 3′-labeled withbiotin, in binding buffer (10 mM HEPES pH 7.3, 20 mM KCl, 1 mM MgCl₂, 1mM DTT, 10% glycerol, 40U RNase inhibitor (RNasin®)) for 30 minutes atroom temperature, and was then cross-linked with UV light (254 nm) for10 minutes on ice. Binding reactions were then washed with PBS and theIRE-IRP complex was eluted from the resin. After separation byelectrophoresis and transfer to a membrane, IRP was detected using mouseanti-HA antibody. The results are shown in FIG. 7. Lane 1 is 5 μl HA-IRPIVT lysate, lane 2 is 25 μl flow-through fraction, lane 3 is 50 μl washfraction, and lane 4 is 25 μl eluted fraction.

The ability of the biotin-labeled RNA to enrich for RNA:proteincomplexes using an immobilized streptavidin sensor chip was examinedusing Biacore™ Surface Plasmon Resonance (SPR). The results are shown inFIG. 8 where the solid line is control mRNA and the dashed line is areference (flow cell 1); and where A=biotinylated RNA template controlloading; B=RNA Pol II injection; C=RNA Pol II bound to control RNA; andD=injection of unlabeled control RNA. Biotin-labeled control RNA wascaptured on a Streptavidin-coated sensor chip followed by injection ofbacterial RNA Polymerase. A binding response of RNA polymerase II wasdetected on the active RNA surface and specificity was confirmed by theloss of binding after injection of non-labeled control RNA. Twenty pmollabeled RNA was diluted into nuclease-free HEPES buffer (pH 7.3),injected at 5 l/min for four minutes, and captured onto a commerciallypurchased streptavidin-coated sensor chip for the Biacore 3000®.Bacterial RNA polymerase (0.1 U/μl) was then injected for two minutes.As shown in FIG. 8, a binding response of RNA polymerase II was detectedon the active RNA surface and specificity was confirmed by loss ofbinding after injecting non-labeled control RNA. Specificity wasdetermined through competition of binding RNA polymerase with a 50-100fold excess of non-labeled RNA polymerase template RNA that was injectedfor four minutes.

Poly(A)₂₅ RNA was labeled usingdesthiobiotin-PEG₄-alkane-3′5′-bisphosphate cytidine and T4 RNA ligase.The Poly(A) Binding Protein (PABP), which binds the poly(A) tracts ofmRNA is ubiquitous and readily detectable in cell culture lysates. Thelabeled RNA (50 pmol) was incubated with streptavidin magnetic beads(0.5 mg) for thirty minutes in 20 mM Tris-HCl (7.5), 100 mM NaCl, 1 mMEDTA. After washing, the beads were then incubated with 100 mg of HEK293 cell lysate in Binding Buffer (10 mM Tris-HCl, pH 7.5, 2.5 mM MgCl₂,10 mM KCl, 15% glycerol, 0.5% Tween-20, and 10 μg tRNA) for one hour at4° C. An unrelated RNA was used as a negative control, and beads wereincubated with lysate alone to assess background. Beads were washed in20 mM Tris-HCl (7.5), 10 mM NaCl, 0.5% Tween-20, and protein was elutedby heating at 95° C. for 5-10 minutes using 1× reducing sample buffer,or eluting with 4 mM biotin in 20 mM Tris (7.5). After separation byelectrophoresis, PABP was detected using PABP antibody.

The results are shown in FIGS. 14 and 15. Synthetic RNA (50pmol/reaction) was end-labeled using a twenty-fold excess ofdesthiobiotin-PEG₄-alkane-3′5′-bisphosphate cytidine with T4 RNA ligase.Labeled RNA was incubated with 0.5 mg streptavidin magnetic beads forthirty minutes at room temperature. Beads were then washed 2× in 20 mMTris (7.5). For the binding reaction, HEK 293 cell lysate (100 μg) wereincubated with RNA-containing beads (both positive and negativecontrols), or base beads in 1× binding buffer (PABPC1-10 mM Tris (7.5),2.5 mM MgCl₂, 10 mM KCl, 15% glycerol, 0.5% Tween-20, 10 μg tRNA;SNRPA1-10 mM Tris (7.5), 250 mM NaCl, 1 mM EDTA, 0.5% Tween-20, and 10μg tRNA) for 1 hour at 4° C. Beads were washed 3× in 20 mM Tris (7.5),10 mM NaCl, 0.5% Tween-20. Complexes were eluted using 2× reducingsample buffer. Normalized samples were separated by electrophoresis,transferred, and detected using PABPC1, GST (SNRPA1) antibodies (1:1000dilution in TBST-0.5% BSA). Exposure time—1 minute. FT flow-through; 1,2, 3—washes, E—elution. RNA used for pull-downs are labeled aboverespective blots. Lane 1—flow-through (40 μl), Lanes 2-4—washes (40 μl),Lane 5 elution (20 μl).

EXAMPLE 4

In one embodiment, biotin or other suitable moiety containing n alkanelinkage and PEG₁₂ spacer, known by one skilled in the art, on thelabeled nucleotide serves as an affinity handle for isolatingRNA:protein complexes. The functionality of a described biotin-labeledRNA to serve as an affinity handle for isolating RNA complexes(containing RNA, DNA, RNA and DNA, or protein) using an affinity resin,was determined using streptavidin magnetic beads.

Poly(A)₂₅ RNA was labeled using biotin-PEG₁₂-alkane-3′5′-bisphosphatecytidine and T4 RNA ligase. The Poly(A) Binding Protein (PABP), whichbinds the poly(A) tracts of mRNA, was cloned into a vector containing aGST-tag and expressed in a human cell-free in vitro translation (IVT)system. The lysate was diluted 1:10 for use in the binding reaction. Thelabeled RNA (50 pmol) was incubated with streptavidin magnetic beads(0.5 mg) for thirty minutes in 20 mM Tris-HCl (7.5), 100 mM NaCl, 1 mMEDTA. After washing, the beads were then incubated with 2-3 μl ofdiluted IVT lysate cell lysate in Binding Buffer (10 mM Tris-HCl, pH7.5, 2.5 mM MgCl₂, 10 mM KCl, 15% glycerol, 0.5% Tween-20, and 10 μgtRNA) for one hour at 4° C. An unrelated RNA was used as a negativecontrol, and beads were incubated with lysate alone to assessbackground. Beads were washed in 20 mM Tris-HCl1 (7.5), 10 mM NaCl, 0.5%Tween-20, and protein was eluted by heating at 95° C. for 5-10 minutesusing 1× reducing sample buffer, or eluting with 4 mM biotin in 20 mMTris (7.5). After separation by electrophoresis, PABP was detected usingPABP antibody.

Results are shown in FIG. 16. Synthetic RNA (50 pmol/reaction) wasend-labeled using a twenty-fold excess ofBiotin-PEG₁₂-Alkane-3′5′-Bisphosphate Cytidine with T4 RNA ligase.Labeled RNA was incubated with 0.5 mg of streptavidin magnetic beads forthirty minutes at room temperature. Beads were then washed 2× in 20 mMTris (7.5). PABPC1-GST and SNRPA1-GST proteins were expressed usinghigh-yield human intro translation lysate. Lysates were diluted 1:10 inbinding buffer before use. For the binding reaction, proteins wereincubated with RNA-containing beads (both positive and negativecontrols), or base beads in 1× binding buffer (PABPC1-10 mM Tris (7.5),2.5 mM MgCl₂, 10 mM KCl, 15% glycerol, 0.5% Tween-20, 10 μg tRNA;SNRPA1-10 mM Tris (7.5), 250 mM NaCl, 1 mM EDTA, 0.5% Tween-20, and 10μg tRNA) for one hour at 4° C. Beads were washed 3× in 20 mM Tris (7.5),10 mM NaCl, 0.5% Tween-20. Complexes were eluted using 2× reducingsample buffer. Normalized samples were separated by electrophoresis,transferred, and detected using PABPC1, GST (SNRPA1) antibodies (1:1000dilution in TBST-0.5% BSA). Exposure time—1 minute. FT—flow-through; 1,2, 3—washes, E—elution. RNA used for pull-downs are labeled aboverespective blots. Lane 1—flow-through (40 μl), Lanes 2-4—washes (40 μl),Lane 5—Elution (20 μl). Similarly, U1A RNA was labeled, and a GST-taggedSNRPA1 was overexpressed in the IVT system. The RNA-bound beads wereincubated with the 2-3 μl of the IVT lysate in binding buffer (10 mMTris-HCl, pH 7.5, 250 mM NaCl, 0.5% Tween-20, 1 mM EDTA, and 10 μg oftRNA) for one hour at 4° C. The results are shown in FIG. 16. RNA usedfor pull-downs are labeled above respective blots. Lane 1—flow-through(40 μl), Lanes 2-4—washes (40 μl), Lane 5—Elution (20 μl).

EXAMPLE 5

In one embodiment, biotin or another suitable moiety containing a PEG₁₂spacer, known by one skilled in the art, on the labeled nucleotideserves as an affinity handle for isolating RNA:protein complexes. Thefunctionality of a described biotin-labeled RNA to serve as an affinityhandle for isolating RNA complexes (containing RNA, DNA, RNA and DNA, orprotein) using an affinity resin, was determined using streptavidinmagnetic beads. In this embodiment, the protein was crosslinked to theRNA for enrichment.

Poly(A)₂₅ RNA was labeled using biotin-PEG₁₂-alkane-3′5′-bisphosphatecytidine and T4 RNA ligase. The Poly(A) Binding Protein (PABP), whichbinds the poly(A) tracts of mRNA, was cloned into a vector containing aGST-tag and expressed in a human cell-free in vitro translation (IVT)system. The lysate was diluted 1:10 for use in the binding reaction. Thelabeled RNA (50 pmol) was incubated with streptavidin magnetic beads(0.5 mg) for thirty minutes in 20 mM Tris-HCl (7.5), 100 mM NaCl, 1 mMEDTA. After washing, the beads were then incubated with 2-3 μl ofdiluted IVT lysate cell lysate in Binding Buffer (10 mM Tris-HCl, pH7.5, 2.5 mM MgCl₂, 10 mM KCl, 15% glycerol, 0.5% Tween-20, and 10 μgtRNA) for one hour at 4° C. An unrelated RNA was used as a negativecontrol, and beads were incubated with lysate alone to assessbackground. After a gentle wash, the binding reaction was crosslinked onice using UV light. Beads were washed in 20 mM Tris-HCl (7.5), 10 mMNaCl, 0.5% Tween-20, and protein was eluted by heating at 95° C. forfive to ten minutes using 1× reducing sample buffer, or eluting with 4mM biotin in 20 mM Tris (7.5). After separation by electrophoresis, PABPwas detected using GST antibody.

The results are shown in FIG. 17. Methods are described for FIG. 16except that after a gentle wash after the binding reaction, RNA-proteincomplexes were crosslinked for ten minutes on ice. Exposure time—30seconds. FT—flow-through; 1, 2, 3—washes, E elution. RNA used forpull-downs are labeled above respective blots. Lane 1—flow-through (40μl), Lanes 2-4—washes (40 μl), Lane 5—Elution (20 μl).

All citations are expressly incorporated by reference herein in theirentirety, including those throughout the disclosure as well as thefollowing:

-   Khanan et. Al. (2006) Poly(A)-Binding Protein Binds to A-Rich    Sequences via RNA Binding Domains 1+2 and 3+4. RNA Biology. 3:    170-177.-   Rimmele and Belasco. (1998) Target discrimination by RNA binding    proteins: role of the ancillary protein U2A′ and a critical leucine    residue in differentiating the RNA-binding specificity of    spliceosomal proteins U1A and U2B″. RNA. 4: 1386-1396.-   DNASU Plasmid Repository, Arizona State University BioDesign    Institute.-   U.S. Patent Publication No. 2011/0262917.-   England et al. Specific labeling of 3′ termini of RNA with T4 RNA    ligase (1980) Methods Enzym. 65: 65-74.-   Brennan and Gumport. T4 RNA ligase catalyzed synthesis of    base-analogue-containing oligodeoxyribonucleotides and a    characterization of their thermal stabilities. (1985) Nucleic Acids    Res. 13: 8665-8684.-   Hinton et al. The preparative synthesis of oligodeoxyribonucleotides    using RNA ligase. (1982) Nucleic Acids Res. 10:1877-1894.-   Walker et al. T4-induced RNA ligase joins single-stranded    oligoribonucleotides (1975) PNAS 72: 122-126.-   Richardson and Gumport. Biotin and fluorescent labeling of RNA using    T4 RNA ligase. (1983) Nucleic Acids Res. 11: 6167-6184.-   England et al. Dinucleoside pyrophosphates are substrates for    T4-induced RNA ligase (1977) PNAS 74: 4839-4842.-   Keith. Optimization of conditions for labeling the 3′ OH end of tRNA    using T4 RNA ligase. (1983) Biochimie 65: 367-70.-   Romaniuk et al. Joining of RNA molecules with RNA ligase (1983)    Methods Enzym 100: 52-59.-   Romaniuk et al. The effect of acceptor ribonucleotide sequence for    the T4 RNA ligase reaction. (1982) European J of Biochem. 125:    639-643.-   Park et al. Useful tools for biomolecule isolation, detection, and    identification: acylhydrazone-based cleavable linkers. (2009)    Chemistry & Biology 16: 763-772.-   Shigdel et al. Diazirine-based DNA photo-cross-linking probes for    the study of protein-DNA interactions (2008) Angew. Chem. Int. 47:    90-93.-   Costas et al. RNA-protein crosslinking to AMP residues at internal    positions in RNA with a new photocrosslinking ATP analog (2000)    Nucl. Acids. Res. 28: 1849-1858.-   Gomes and Gozzo (2010). Chemical cross-linking with a diazirine    photoactivatable cross-linker investigated by MALDI- and    ESI-MS/MS. J. Mass. Spectrom. 45:892-9.-   Liu and Sun. Direct isolation of specific RNA-interacting proteins    using a novel affinity medium. (2005) Nucl. Acids Res. 33: 1-5.-   Bachler et al. StreptoTag: A novel method for the isolation of    RNA-binding proteins. (1999). RNA 5: 1509-1516.

The embodiments shown and described in the specification are onlyspecific embodiments of inventors who are skilled in the art and are notlimiting in any way. Therefore, various changes, modifications, oralterations to those embodiments may be made without departing from thespirit of the invention in the scope of the following claims.

What is claimed is:
 1. A method of quantitating a nucleic acid or an oligonucleotide comprising: a) adding to a nucleic acid or an oligonucleotide, a detectable modified nucleotide of structure II:

a salt, a conjugate base, a tautomer, or an ionized form thereof, wherein Base* is a purine or pyrimidine base; R is H, OH, CH₃ or a hydroxyl protecting group; Alk is a connecting group having the structure -//—(CH₂)_(m)—Y—//- wherein Y is a bond or bond forming group selected from

and m is an integer ranging from 3 to 6 inclusive, and wherein the leftmost bond is to Nus and the rightmost bond is to Lnk; Lnk is a linking group having the structure

wherein n is an integer ranging from 2 to 48 inclusive; A₁ is a bond forming group selected from

A₂ is a bond forming group selected from

A₃, when present, is a bond forming group selected from

and X is a cleavable group that can undergo silicon-carbon cleavage, nucleophilic cleavage, redox cleavage, photochemical cleavage, enzymatic cleavage, or exchange-based cleavage; Z is a branching group that contains a crosslinking agent; and the leftmost bond is to Alk and the rightmost bond is to Obs; and Obs is an observable label; and b) quantitating the nucleic add based on quantifying the detectable modified nucleotide.
 2. The method of claim 1, wherein one molecule of the observable detectable label is added per oligonucleotide or nucleic acid.
 3. The method of claim 1, wherein the observable label is a chromogen, a fluorophore, a mass label, a spin label, a mass tag, a streptavidin-binding label, biotin, a derivative of biotin, desthiobiotin, an azide, an alkyne, an aldehyde, a diene, an amine, a hydrazide, a disulfide, a polyethyleneglycol (PEG), or a secondary detection label.
 4. The method of claim 1, wherein the nucleic acid is a RNA or the oligonucleotide is a ribonucleotide.
 5. The method of claim 1, wherein the oligonucleotide or the nucleic acid is added to the detectable modified nucleotide by ligation, nick translation, random priming, polymerase chain reaction (PCR), 3′-end labeling, or by transcribing RNA using SP6, T3, or T7 RNA polymerases.
 6. The method of claim 1, wherein the nucleic acid is a RNA and the detectable modified nucleotide is added by: heating RNA in a solution, the solution optionally containing dimethylsulfoxide at a concentration up to 25%, to a temperature of about 75° C. to about 95° C. then cooling the heated RNA for at least one minute to less than 10° C., and, contacting the heated and cooled RNA with the detectable modified nucleotide of structure (II) under reaction conditions using T4 RNA ligase and including PEG having molecular weight between about 1500 and 24,000 inclusive and at a concentration ranging from 5% PEG to 20% PEG inclusive to ligate the compound of structure (II) to the RNA to result in a detectable modified RNA.
 7. The method of claim 6, wherein the concentration of PEG is about 15%.
 8. The method of claim 6, wherein the molecular weight of PEG is 20,000.
 9. A method for assaying a ribonucleic acid (RNA) analyte, the method comprising: a) labeling an RNA with the detectable modified nucleotide of structure (II)

a salt, a conjugate base, a tautomer, or an ionized form thereof, wherein Base* is a purine or pyrimidine base; R is H, OH, CH₃, or a hydroxyl protecting group; Alk is a connecting group having the structure -//—(CH₂)_(m)—Y—//- wherein Y is a bond or bond forming group selected from

and m is an integer ranging from 3 to 6 inclusive, and wherein the leftmost bond is to Nus and the rightmost bond is to Lnk; Lnk is a linking group having the structure

wherein n is an integer ranging from 2 to 48 inclusive; A₁ is a bond forming group selected from

A₂ is a bond forming group selected from

A₃, when present, is a bond forming group selected from

and X is a cleavable group that can undergo silicon-carbon cleavage, nucleophilic cleavage, redox cleavage, photochemical cleavage, enzymatic cleavage, or exchange-based cleavage; Z is a branching group that contains a crosslinking agent; and the leftmost bond is to Alk and the rightmost bond is to Obs; and Obs is an observable label; to form a modified RNA probe, b) contacting the modified RNA probe with a sample containing the RNA analyte under conditions to hybridize the modified RNA probe with the RNA analyte, and c) detecting the RNA analyte hybridized with the modified RNA probe, wherein hybridization and detection of the modified RNA probe assays the RNA analyte.
 10. The method of claim 9 wherein the assay is chosen from at least one of mobility shift, Northern blot, pull-down assay, protein-RNA interaction, and in situ hybridization.
 11. The method of claim 9 wherein the detection uses a streptavidin-conjugated reporter molecule.
 12. The method of claim 11 wherein the reporter molecule is an enzyme, a fluorescent compound, an isotope, a gold particle, or combinations thereof.
 13. The method of claim 1, wherein the nucleic acid or oligonucleotide is bound to or interacts with a protein.
 14. The method of claim 13, wherein the protein is an RNA binding protein or a protein that can interact with a RNA.
 15. The method of claim 1 wherein the detectable modified nucleotide is chosen from


16. The method of claim 9 wherein the detectable modified nucleotide is chosen from 